Questions tagged [fastq]
FASTQ is a file format use to store short reads and their quality values
63
questions
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1answer
46 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
46 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
38 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 ...
0
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0answers
13 views
Programmatic Access to `fastq-load.py` Arguments in SRR Metadata
Is there a way to programmatically access the fastq-load.py arguments from the SRR metadata?
Specifically I would like to capture the exact command line arguments ...
2
votes
2answers
108 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
63 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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4
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4answers
103 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
28 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
31 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
votes
2answers
88 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:
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0
votes
1answer
73 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 +...
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0answers
17 views
Could I create assembly by unicycler for ion torrent output?
I have ubam files from ion torrent machine, I convert it to fastq by samtools bam2fq tool, then I use galaxy platform to assembly the genome by Unicycler. At the end I get a fasta file.
My question ...
0
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1answer
227 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 ...
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0answers
50 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
96 views
0
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1answer
92 views
How to convert a .fastq chip-seq file into a wig/bigwig track and how to extract chip-seq peaks?
I have a reference .fasta file and a raw .fastq file with chip-seq data. I am trying to create a bigwig track from the and .fastq and .fasta ref file of the raw signal. Then I would like to do some ...
0
votes
1answer
103 views
How to remove degenerate sequence (N4) at the 5' and 3' of the reads?
I have to analyse GSE114327. For that, I use GSE instruction based on GSM3139597.
In that data processing section has written:
FASTQ reads were subjected to adapter removal (cutadapt) per ...
2
votes
2answers
184 views
Filter reads belonging to unique sequences with threshold
I have CLL samples as fastq files and I want to remove those reads which have a unique sequence with less than 10 read counts each. I tried this by following way using awk to make it faster:
...
6
votes
1answer
480 views
Convert BAM to properly paired FASTQ files
I thought I had figured this one out. But apparently not.
I need to convert a BAM file of paired-end alignments to two FASTQ files of paired reads to realign them, with a twist: I only want reads ...
3
votes
2answers
269 views
What do the FASTQ file names mean here?
I would like to run an analysis on Nanopore data. I'm trying to download sample data from https://github.com/nanopore-wgs-consortium/chm13. I would like to run minimap on the FASTQ files, resuling in ...
3
votes
1answer
160 views
Fast processing of fastq data
I am trying to write python script for customized filtering for fastq file (size >3 GB). My proposed script is as follows:
...
3
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0answers
38 views
Determine reference for reference-compressed SRA file
I have 241 SRA files that appear to be reference compressed. I didn't even know this was a thing until I tried to convert them to Fastq files without an internet connection. I got the "name not found ...
2
votes
2answers
171 views
Frequency of specific viral sequence in .BAM or .fastq
I was wondering if anyone had any experience 'counting' the frequency of a particular viral sequence in an individual's fastq sequence. So basically, counting the number of occurrences of a particular ...
1
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5answers
206 views
Testing for viral/bacterial infection FASTQ files
What's the best way to test if a pair of Illumina FASTQ files from blood DNA extraction contain any reads from viral/bacterial infection from DNA in human blood? Thanks in advance.
EDIT:
Looking at ...
1
vote
1answer
107 views
Batch alignment of inconsistently named Fastq files
I have numerous gzip-compressed paired-end Fastq files with ChIP-seq data that I would like to align with bowtie2. I confirmed that bowtie2 takes .gz files, ...
1
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0answers
43 views
“Bad substitution” error while trimming adapters [closed]
I have this script to trim adaptors from my fastq sequencing files
for PAIR in $(fastq | sed 's/_R.//g' | uniq)
I am gitting this error: bad substitution
Could ...
3
votes
2answers
124 views
Getting data from fastq by generator
I have a task in a training that I have to read and filter the 'good' reads of big fastq files.
I downsampled, got the code working, saving in a python dictionary. But turns out the original files ...
0
votes
1answer
122 views
Where to Download Cancer Raw Reads (fastq)?
Does anyone know where I can download cancer raw reads (fastq files), tumor and Germline for non-humans?
I wanted to make a study with human data but I don't have the control access to download raw ...
1
vote
1answer
94 views
Non-random access on a fastq file
There was a nice question on random access on a fastq file, however I have the opposite problem. I want to programatically access non-random fastq entries quickly (using C++).
Say I have several ...
9
votes
1answer
570 views
Why does this human bam file only have one copy of each chromosome?
As we know that in human DNA sequence, one copy of chromosome comes from mother's DNA and another copy comes from father's DNA so as to form two copies of each chromosome in human DNA. So, if we ...
7
votes
1answer
294 views
Multithread fastq processing with kseq.h in C++11?
Background
I am using the wonderful kseq.h as my fastq/fasta parser for a C++ project. My actual implementation uses something like this, where I am counting kmers ...
1
vote
1answer
77 views
Are there free cloud computing platforms for biology projects? [duplicate]
I want to implement the analysis found in the paper RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics The project id is 281708. ...
6
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5answers
585 views
Delete all 4 lines of a fastq read from a fastq file using read ID
I have the following error when running bowtie2:
Error: Read HWI-D00466:116:CC62WANXX:3:1102:7363:63646 1:N:0:GCACACG
has more read characters than quality values.
I now want to remove all 4 ...
4
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2answers
139 views
How to align output of grep --color=always? (To QC fasta/fastq files)
Grepping out short sequences from a fasta or fastq file is a really useful way to look at sequencing data. Using the option --color=always makes this even more ...
5
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3answers
2k views
Bash scripting FastQC for multiple fastq files in multiple directories
I am completely new to bioinformatics so I'm looking to learn how to do this.
I have multiple directories with fastq files: E.g; 10 Directories with each time series, each with Treatment and control ...
0
votes
1answer
187 views
Fastqc- Per Base Sequence Quality
I am trying to figure out how to interpret the "Per Base Sequence Quality"? What does Position in reads (bp) mean? Also in order to draw this box-plot graphics, more than one quality scores are needed ...
2
votes
2answers
158 views
filter out FASTQ reads which are shorter
I tried to filter out FASTQ reads which are shorter than 259 bp with
...
3
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2answers
3k views
2
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2answers
75 views
fuse fastq files with multiple records
I'd like to fuse ~50 pairs of corresponding fastq files on per sequence bases. I'd be happy for a solution as a Linux script, R script (if feasible with huge files), or any free software that runs ...
-1
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2answers
414 views
Script to run everything in a loop for extracting tar.gz files into fastq and to bam with alignment?
Original tar.gz files look like below:
...
8
votes
1answer
269 views
Counting repeated kmers sequences that match at least x % of reads sequence
Working on a fastQ file, I would like to get the occurrences of repeated sequences for all possible kmers of a given length that cover at least 90% of the read's length for the whole data set.
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8
votes
1answer
282 views
How to get the count of each kmer past 255 using khmer
I have a Fastq file and I want to get the exact count of each possible kmer from this file.
On a previous post called How to use khmer to count k-mers? Daniel Standage proposed a custom script based ...
2
votes
1answer
64 views
efficient counting of dinucleotides/trinucleotides on fastq reads?
What's an efficient way of counting of dinucleotides/trinucleotide pattern on fastq.gz file reads?
I know there are tools like seqtk that will be very efficient at reading through the .fastq.gz files,...
5
votes
1answer
1k views
5' and 3' bias in Rna-seq data
I'm working with rna-seq samples. I see 5' bias and also 3' bias in the per-base sequence content plot. From this link I see that the bias at the start of the sequences appears to be the result of ...
3
votes
3answers
444 views
How to demultiplex pair-end fastq reads with barcode 2 in the identifier line?
I have multiplexed pair-end fastq reads with dual barcodes. The issue is that one barcode is present in the header and one is present at the beginning of the read. I need a method to demultiplex this ...
3
votes
1answer
105 views
Can the canu assembler output a fastq file of the final assembly just like HGAP4?
I have assembled some genome from Sequel PacBio data both with HGAP4 on the SMRT Link interface and using canu on the command line. The HGAP4 assembler outputs a fastq file of the final assembly such ...
7
votes
2answers
239 views
Canu assembly not making a single consensus?
I've downloaded reads from this BioProject. Using canu with default parameters (no correction), I've got 4 contigs, none of which really look like the reference plasmid here.
The command I used was:
...
4
votes
1answer
830 views
Estimating BAM file from compressed fastq file size
Is there a way to estimate the size of a BAM file will have after mapping with BWA?
The input file are two mates fastq files, compressed with gzip, each one about 70G.
4
votes
2answers
214 views
Is there a way to quickly verify the presence of some SNPs in Fastq files?
Is there a tool that can scan fastq files without assembling them for a custom list of user defined snps?
7
votes
1answer
269 views
Split FASTQ and matching BAM into matching chunks
I am running a slow downstream analysis on a large set of nanopore reads (approx 3 million), and would like to split them into smaller chunks, run the analysis in massively parallel, and then ...
