Questions tagged [fastq]

FASTQ is a file format use to store short reads and their quality values

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Good / recommended way to archive fastq and bam files?

We have a lot of Illumina sequenced exome data. Currently we are using spring for its great lossless compression, but we are looking if there is anything better (and most preferably opensource) which ...
Karthik Nair's user avatar
2 votes
2 answers
89 views

How to differentiate DNA fastq and RNA fastq files?

I have 2 sets of fastq files from another collaborator. The first is contains exome data and the second contains RNAseq data. But both have the RNA in the name but a different ID. How do I ...
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1 answer
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Running cellranger on scRNASeq data with feature barcoding (10x + antibody capture)

I can't seem to find a clear answer to this question, so here it goes: I have sequenced scRNASeq + scVDJSeq (TCR) data, which has been sequenced using feature barcoding from 10x genomics, via antibody ...
h3ab74's user avatar
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2 votes
1 answer
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Can we test the accuracy of Phred scores shown in FASTQ files

Recently I have ran a human WGS on the BGI DNBSEQ system, and their FASTQ quality scores seem to be quite impressive, where the Phred scores barely deteriorate along the read length when checked on ...
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DNASTAR viral-host integration assembly keeps failing

I have two NGS files from an NGS company corresponding to the sequencing data from a tumor sample as follows: TB_7710391_R1.FASTQ.gz TB_7710391_R2.FASTQ.gz I have downloaded the genome for MCPyV as ...
InterestingQuestions61's user avatar
1 vote
2 answers
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How can I detect MCPyV in a FASTQ file?

I have received two NGS files from an NGS company, both are FASTQ files that correspond to reads from a tumor sample. I heavily suspect that MCPyV is present, and I am hoping to identify it. What ...
InterestingQuestions61's user avatar
1 vote
1 answer
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Remove files after process is terminated

In my pipeline nextflow, I create a channel with channel.fromSRA and the channel contains lots of heavy files.fastq.gz. Then I have a first process to unzip files and transform them in files.fasta and ...
eva fonta's user avatar
4 votes
4 answers
334 views

How to get a file with the number of reads for several fastq.gz files?

I have generated several FASTQ files and I would like to know the amount of reads for each of them. I am planning to run FastQC on the files which I know would give me the number of reads per sample ...
pythonbeginner's user avatar
2 votes
1 answer
163 views

Remove low quality reads

I want to remove reads from FASTQ file that contain homopolymers > 10bp and remove reads with <35 average quality score across the entire read. To remove homopolymers > 10bp, I tried this on ...
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2 votes
1 answer
283 views

If fastp output is not a good measure of FASTQ correctness, what is?

In the beginning of my pipeline, I just fed the paired reads (2 files) into fastp, with the default options, and assumed it would do a good job preparing the reads for the next step: alignment But I ...
fullmooninu's user avatar
3 votes
1 answer
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CRISPR genome wide screen analysis using MAGeCK-- Loss of reads/sgRNA using MAGeCK count function?

Sorry if this question seems basic. I am trying to run the MAGeCK pipeline to analyze CRISPR knockout screen data produced by someone in my lab around 5 years ago. I was given the data as bam files ...
Cassie Bishop's user avatar
1 vote
1 answer
277 views

Comparison of fastq files reads

My goal is to compare reads from two different fastq files on a Linux machine. The following are the comparisons to perform: How many common reads are between the two fastq files? How many reads are ...
utr's user avatar
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3 votes
2 answers
102 views

What can be the bias of aligning paired-reads in a single-end mode?

I don't know if I'm in the right place but I have a technical problem to fix. I would have to align paired-end reads from Illumina sequencing to compare a normal genome with a tumor one. When I align ...
cucalorda's user avatar
2 votes
2 answers
60 views

Sequence format: grouping sequences within a flat file

Is there a sequence format allowing multiple sequences to be grouped across a flat file? The specific application is stacking separate nucleotide sequences against a given RNA secondary structure. To ...
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1 answer
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Aligning scRNA-seq fastq to .bam without cell barcodes

I would like to convert the fastq files from this dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98679 to .bam files. The group did not provide the scripts they used to to their ...
Angus Campbell's user avatar
1 vote
2 answers
215 views

Converting .bw files to .fq (fastq)

I am able to convert .bw files to .fq(fastq) manually in Shell, but I would like to automate the process coz I have hundreds of .bw file that I need to convert. Till now, I could think of following ...
Sam's user avatar
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0 votes
1 answer
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Pipeline for paired end RNA sequence data to proteins

Forgive the basic question here, but I'm super novice at this ... I have a series of paired-end RNA fastq files (e.g. SRR10720226_1.fastq.gz and ...
agf1997's user avatar
  • 101
3 votes
1 answer
277 views

Multiple file Python script

I am currently doing an analysis requiring a multiple-input script. I have a directory filled with 900+ samples. Each sample is comprised of two-files in a fastq format. This is an example of a sample:...
pvp's user avatar
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1 vote
0 answers
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Removing adapters + primers from fastq files

I am currently in the process of removing adapters and primers from some 16S data acquired, and have a conceptual question regarding this pre-processing step: So there are a series of different primer ...
h3ab74's user avatar
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1 vote
2 answers
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10X low rate of correct barcodes was observed for the candidate chemistry choices for the input

I am testing a 10x fastq dataset , but cellranger count complains "An extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input", I have tried ...
ciwei's user avatar
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1 answer
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fastqCleaner failing to launch in RStudio

When I execute: > FastqCleaner:::launch_fqc()() I get the following output ...
Leon Lenzo's user avatar
0 votes
2 answers
304 views

How to compare sequences of genes obtained after whole-genome sequencing to reference genome?

My idea is to align whole-genome sequencing data (as fastq files after, 30× coverage, gDNA) to the reference mouse genome (NCBI), extract the immunoglobulin locus and compare it to the reference. I ...
abc's user avatar
  • 101
2 votes
1 answer
171 views

When using cutadapt, can I specify an R2 adapter as optional when I have a required R1 adapter?

I'm using cutadapt 3.5 to trim adapters and perform some filtering on paired-end data. Both R1 and R2 sequences have 3' adapters that might be found depending on the sequence length, but R1 also has ...
Jesse's user avatar
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2 votes
0 answers
67 views

Bowtie2 gets stuck on alignment

I am aligning a fastq file as follows: ...
justinian482's user avatar
1 vote
0 answers
110 views

I can't launch FastqCleaner I always get a warning message and the application never starts

I tried to install all the needed and related packages but I still did not know what the problem is, Can anyone please help if anything else I can do?? I always get this over and over: ...
Ruba Mahmoud's user avatar
1 vote
1 answer
152 views

Translate all reads in a .fastq into protein sequence from deep mutational scanning experiment

I'm working with paired-end NGS reads from an Illumina platform. The sequences I have are all of the same gene, but have one or more substitution mutations each. Here is a rough workflow for ...
Paul's user avatar
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2 votes
1 answer
120 views

How to determine NCBI's SRS google cloud bucket or AWS bucket

It appears that AWS and GCP host SRA data and it's beneficial to grab the data from that source when running on GCP for example. Given an SRR accession like SRR1929796 https://trace.ncbi.nlm.nih.gov/...
Dougnukem's user avatar
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0 answers
74 views

How likely is it to find primers sequences in already-trimmed reads?

So, I am analysing 18S amplicon data (fastq files) to be able to eventually investigate the taxa composition. After removing primers (using cutadapt) from both R1 ...
gabt's user avatar
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0 votes
1 answer
104 views

Error when using awk command to trim sequence files

I am attempting to edit my fastq sequence files with an awk command from a published article. The sequence files are all ...
Justin1609's user avatar
1 vote
1 answer
381 views

How to convert multiple single-end bam files to fastq using samtools

Hi I am trying to convert bam files generated from Ion Torrent Proton sequencing to fastq format so that I can upload them to ...
Justin1609's user avatar
0 votes
1 answer
709 views

Converting Fastq files to Fasta files on Ubuntu

I am new to bioinformatics and programming. I tried to convert my fastq files to fasta file, but got this. What could be wrong? ...
Greater's user avatar
1 vote
3 answers
2k views

Compressing read data (converting fastq to fastq.gz) on Windows

I downloaded some of my data in fastq format instead of fastq.gz. I want to upload my data on a server now. I was wondering if there is a way to convert my fastq files to fastq.gz on windows (I read ...
Tarannom's user avatar
0 votes
1 answer
81 views

Impact of merging ChIP-seq runs of the same sample on PCR duplicates identification?

I'd like to a follow up question to this question related to merging fastq files for ChIP-seq. Let's assume we have one sample library that is re-sequenced two or three times in order to achieve a ...
Ni-Ar's user avatar
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1 vote
2 answers
266 views

How to convert CRAM file with 10x data in three fastq files

10x Genomics data are stored in three FASTQ files, besides the standard R1 and R2 reads, there is also a I1 file with some metadata. Sometimes however they are shipped in a single bam/cram file (e.g. ...
1 vote
3 answers
150 views

Finding smaller sequences from within larger sequences

I am currently working with fastq files which have hundreds of thousands of lines of text. However, not all of them are sequences I am interested in. My sequences are in one line and have a fixed ...
Jean Luc's user avatar
2 votes
2 answers
271 views

Get frequency of index sequences of fastq file

I recently did some sequencing on a MiniSeq and unexpectedly the Undetermined_S0_L001_R1_001.fastq.gz file contained quite a lot of data (about 40% of total). I ...
justinian482's user avatar
1 vote
1 answer
602 views

How to convert txt.gz into fastq.gz?

I'm a newbie to bioinfo. I'm trying to use galaxy.networkanalyst.ca for the analysis of RNA-Seq data and for that I need to convert txt.gz files into fastq.gz files. Link: GSM4273445 is one sample ...
Tyto alba's user avatar
  • 123
0 votes
1 answer
207 views

Demultiplexing FASTQ file without index information

I am trying to understand how data that was uploaded to SRA (https://www.ncbi.nlm.nih.gov/sra?LinkName=biosample_sra&from_uid=4510743) can be analyzed with the assumption that the FASTQ file ...
Geo Vogler's user avatar
4 votes
1 answer
73 views

Telling grep to treat N as [ATCG]

Okay so I'm using grep to try and get a preview of some trimming operations that are not going as expected.. Lets say that my sequence in the FastQ file is: ATNGCNATCG What I want to do is.. ...
RPINerd's user avatar
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2 votes
2 answers
468 views

Fastq: how can I check if they are from DNA or RNAseq data?

I have (gave me) Illumina fastq files, which I want to use for variant calling, and I do not know if they are DNAseq or RNAseq data. How can I check this? I do not have any report or who to ask. Many ...
Emma Athan's user avatar
0 votes
0 answers
43 views

How do you determine the strandedness of a RNAseq dataset? [duplicate]

How do you verify if a RNAseq dataset is unstranded, stranded or revesely stranded from a fastq file?
indigoblueraspberry's user avatar
4 votes
1 answer
310 views

Find pattern that is present twice and allow <=2 mismatches on each

I have a fastq file of 400,000 reads (so speed is important). In the sequences there are barcodes integrated that should be present twice. Given a barcode, I want to find the sequences that have the ...
nafizh's user avatar
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1 vote
1 answer
53 views

how to repeat records in fastq n times efficiently?

How to iterate/repeat a record n times in a fastq file using bioawk? I wrote a python code using biopython, but it is very very slow. So, I am wondering if I can get some help by using bioawk. Thank ...
Xiaofei Wang's user avatar
0 votes
1 answer
143 views

Nvidia Parabrick fq2bam pipeline error - No such file or directory

I am trying to implement Nvidia-parabrick fq2bam pipeline to process my WES dataset. The reason for opting this pipeline is the huge number of samples (1004) which take many months to process for ...
Lot_to_learn's user avatar
2 votes
1 answer
437 views

Merging several fq.gz files or R1 and R2 classes into a single one

I have the following files: ...
Juan Pablo Aguilar Cabezas's user avatar
0 votes
1 answer
608 views

How to find the number of contigs produced? N50 length in base pairs? N90 length in base pairs?

I am having trouble with some underlying questions about my project. I have ran a Trinity tool to create a trinity.fasta file. To determine some underlying questions, I used the utility asm_stats to ...
AlphaQueUp's user avatar
3 votes
0 answers
32 views

Template files for bioattributes and meta-data [closed]

I am in process of submiting my FASTQ files to the SRA database. I am a little confused about how to fill the biosample attributes and SRA metadata. I would really appreciate if you anyone could share ...
Riya's user avatar
  • 307
1 vote
2 answers
710 views

Can I eject the flow cell MinION from USB port when doing basecalling?

Can I eject the flow cell MinION from USB port when doing basecalling? Because its taking long and its not possible to wait for its finished, will it affects basecalling?
Peter's user avatar
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2 votes
5 answers
2k views

How to measure the total size of a fastq file in base pairs?

Or Kbps/Gbps. It feels like it should be conceptually very simple, but I can't seem to figure out the right combination of keywords to find it via my search engine. Help would be appreciated! I have ...
Laura's user avatar
  • 787
1 vote
3 answers
4k views

Download multiple fastq files using fastq-dump

I want to download the following fastq files at the same time in Salmon: - SRR10611214 - SRR10611215 - SRR10611215 - SRR10611216 - SRR10611217 Is there a way ...
Lily's user avatar
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