Questions tagged [fastq]
FASTQ is a file format use to store short reads and their quality values
72
questions
0
votes
0answers
14 views
Extract Illumina reads that match with respect to their coordinates on the genome from fastq files
I want to use BPP to estimate divergence times and population sizes of a set of species. I have a vcf file with SNPs called from RADseq. The problem is that BPP uses the multi-species coalescent model ...
2
votes
5answers
70 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 ...
1
vote
3answers
74 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
votes
0answers
29 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 ...
-3
votes
1answer
56 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. ...
2
votes
3answers
99 views
0
votes
0answers
51 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
votes
2answers
55 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
94 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
67 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
vote
1answer
57 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
...
0
votes
1answer
43 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
votes
0answers
26 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
118 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.
...
4
votes
2answers
66 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):
...
4
votes
4answers
355 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
44 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
vote
1answer
42 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
220 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
votes
1answer
145 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 +...
0
votes
0answers
20 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 ...
2
votes
1answer
659 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
72 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
votes
2answers
128 views
0
votes
1answer
214 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
139 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
217 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
812 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
379 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
180 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
votes
0answers
41 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
189 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
vote
5answers
230 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
162 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
vote
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
143 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
145 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
95 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
583 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
423 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
78 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
votes
5answers
841 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
votes
2answers
188 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
votes
3answers
3k 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
236 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
198 views
filter out FASTQ reads which are shorter
I tried to filter out FASTQ reads which are shorter than 259 bp with
...
3
votes
2answers
4k views
2
votes
2answers
80 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
votes
2answers
485 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
296 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.
...
