Questions tagged [fastq]
FASTQ is a file format use to store short reads and their quality values
98
questions
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fastqCleaner failing to launch in RStudio
When I execute:
> FastqCleaner:::launch_fqc()()
I get the following output
...
0
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2answers
108 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 ...
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1answer
35 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 ...
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0answers
33 views
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65 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:
...
1
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1answer
52 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 ...
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0answers
17 views
How to determine SRR google cloud bucket or AWS bucket
It appears that AWS and GCP hosts 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/...
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0answers
44 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 ...
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1answer
37 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 ...
1
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1answer
70 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 ...
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1answer
151 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?
...
0
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1answer
255 views
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 ...
0
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1answer
19 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 ...
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1answer
103 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. ...
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3answers
81 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 ...
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0answers
60 views
Could one Align a FastQ data to a reference genome
I need help with the following question :
Given a FastQ data what can we do directly with it ?
Assess it for Quality control
Align it to a reference genome
Call variants
Assemble's genome
My Thoughts ...
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2answers
72 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 ...
1
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1answer
236 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 ...
0
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1answer
68 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 ...
4
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1answer
54 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..
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1
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2answers
139 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 ...
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0answers
41 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?
4
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1answer
112 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 ...
1
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1answer
39 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 ...
0
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1answer
59 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 ...
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1answer
63 views
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1answer
163 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 ...
3
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0answers
25 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 ...
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2answers
182 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?
2
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5answers
719 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 ...
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3answers
1k 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 ...
0
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0answers
79 views
nanopore QC measures on fastq file
I am working with virus nanopore sequencing data. I have to remove host genome from the reads. I want to run the QC on the fastq file after host genome subtraction. I have used nanoplot. It is slow. I ...
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1answer
207 views
Bash script for automatic overlap merging of respective paired-end reads from samples
I have around 300 paired-end files from 150 samples (1 forward and 1 reverse read for each sample). I want to merge (by sequence overlap) respective forward and reverse reads for each of the samples. ...
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3answers
175 views
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99 views
Unable to gunzip fastq files from ENA
I am trying to process fastq files in order to build gene co-expression networks (by following this tutorial). When I download any fastq file from ENA, and try to process it with the command:
...
2
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2answers
203 views
Extracting specific sections from FASTQ determined by positions
Given a FASTQ file, I'd like to generate a new FASTQ file including only certain subsections of the original sequences specified by their positions.
For example, say I want to extract the ...
1
vote
1answer
830 views
How to split FASTQ reads without re-running `fastq-dump`?
I downloaded a few FASTQs from the SRA that were paired-end 76 bp.
When I look at the FASTQs, I get something like this:
...
3
votes
1answer
216 views
What is a proper way for random subsampling of metagenomic data?
Let's say we have a metagenomic sample that is paired-end FASTQ files including 10,000,000 DNA reads collected using shotgun sequencing.
How would one make a random subsample of the mentioned ...
1
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1answer
115 views
processing multiple fastq files with cutadapt
I have DNA sample from 5 pools, having 25 fastq files each. I am running cutadapt to remove the primers using this command
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0
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1answer
102 views
Filtering raw sequencing reads
I have to filter the raw sequencing reads based on the following criteria:
Remove reads containing adapters
Remove reads containing N > 10% (N represents base that could not be determined)
Remove ...
2
votes
2answers
138 views
Why does this naive Python paired Fastq reader work?
I wrote some throwaway code for ingesting paired-end reads from a Fastq file into memory.
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4
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2answers
70 views
Is the quality score of fastq used somewhere besides trimming/fastqc?
In the fastq format every 4k+4-th line contains the positionwise qualityscore (ascii encoded):
...
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4answers
2k views
Convert FASTA to FASTQ with dummy quality scores
I have a FASTA file which I would like to convert into FASTQ format as the tool I want to use my data in requires it in FASTQ format. So dummy quality scores are fine.
Note: I am not using any ...
3
votes
1answer
73 views
Tool for calibrating base quality scores?
A given sequencing machine assigns a 'certainty' to each base call in the form of a per-base quality score (FASTQ format).
I have reads from several machines aligned to the corresponding reference (...
1
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1answer
53 views
Fastq-dump script download X spots or all
Im trying to write a script where an optional input of -X flag can be used, or if that info is not available download all reads.
my script as follow:
...
2
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2answers
819 views
Error with BWA Mem input having multiple fastq files using cat and process substitution
Running BWA Mem on a number of paired end fastq files using process substitution on the inputs results in this error:
...
0
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1answer
279 views
SRA Toolkit execution problem
I am trying to install SRA Toolkit on MacOS, following all the instructions from NCBI website. It is installed but fastq-dump cannot be executed because "cannot execute binary files". I tried "chmod +...
2
votes
1answer
1k views
Fasterq-dump: --split-spot or -concatenate-reads?
After using files that I downloaded from the SRA with fasterq-dump, I realize I am not 100% sure that I have all the data.
I noticed in my downstream analysis that I seem to be missing the .1 and .2 ...
2
votes
0answers
137 views
Nanopore FASTQ header specifications
Is there a specification anywhere for how a Nanopore FASTQ header should be formatted?
I am creating strategies for generating test FASTQ files and would like to ensure I am generating "correct" ...
3
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2answers
285 views
