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Questions tagged [fastq]

FASTQ files are used in bioinformatics to store sequence information and sequencing quality scores.

FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single ASCII character for brevity.

[Wikipedia]

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Why does wget fail when running multiple wget commands targeting the ENA in a single shell script?

I wanted to download FASTQ files associated with a particular BioProject (PRJEB21446) from the European Nucleotide Archive. There is a button to generate and download a shell script containing wget commands for all FASTQ files associated with the…
Sj1993
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How to fix "AttributeError: 'generator' object has no attribute 'nextRead'" issue?

I'm trying to use this code from https://github.com/dayedepps/q30 and I encountered some issues. I tried fixing some of the issues except for one. def stat(filename): reader = fastq.read(filename) total_count = 0 q20_count = 0 …
apcreyes
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How can I check if a file is a real FASTQ (python)?

I have to check if a file is FASTA, FASTQ or none of those. For the FASTA checking i used the module SeqIO from Bio: def is_fasta(filename): with open(filename, "r") as handle: fasta = SeqIO.parse(handle, "fasta") return…
C insi
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Split fasta file into specific new fasta files

So I'm writing this code that will read a fasta file. In the fasta file, there will be 10 sequences. The start of the sequence will be ">" I want to split 50:50 of those sequences and create two new fasta files with it. 5 sequences in one new file;…
Juleszio
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A question on spotting the error.What are the following errors in this python3 script?

#!/usr/bin/env python3 # trimAll.py #Initialize variable to contain the directory of un-trimmed fastq files fastqPath="/scratch/AiptasiaMiSeq/fastq/" #Initialize variable to contain the suffix for the left…
Mrinal Subash
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Trying to create a script that counts the length of a all the reads in a fastq file but getting no return

I am trying go count the length of each read in a fastq file from illumina sequencing and outputting this to a tsv or any sort of file so I can then later also look at this and count the number of reads per file. So I need to cycle down the file and…
Rob
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Merging files in folder with same file name except one character

I have filenames like the…
Jack Arnestad
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Pass lines from 2 files to same subroutine

I'm in the process of learning how to use perl for genomics applications. I am trying to clean up paired end reads (1 forward, 1 reverse). These are stored in 2 files, but the lines match. What I'm having trouble doing is getting the relevant…
aupadhyaya
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ValueError: invalid literal for int() with base 10: '' error occurs when part of larger code, not when alone

defaultdict(, {'match': 1}) [(0, 0)] [] [] [] Traceback (most recent call last): File "Joinomattic_1.py", line 409, in verboseprint (magic(matching)) File "Joinomattic_1.py", line 408, in magic = lambda…
Tom
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Checking my Tuple code

So I'm trying to parce a FastQ sequence, but I'm a beginner to Python, and I'm a little confused as to how to complete my code. This is what the program is supposed to carry out: if I enter the FASTQ seqname…
user3504701
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Read same extension multiple files in one directory in Perl

I currently have an issue with reading files in one directory. I need to take all the fastq files in a file and run the script for each file then put new files in an ‘Edited_sequences’ folder. The one script I had is perl -ne '$i++;…
Shunzhe Yao
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how to extract only mapped reads?

I have mapped a pacbio read against a reference [with minimap2] and now I have my output in Bam file. I would like to extract only the mapped reads from it. I tried bamToFastq [samtools bamtofq input.bam | seqtk seq -A > output.fa], since finally…
azam soltani
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Python Def Syntax Error with . in file name

In my Visual Code Studio running python3.6 - my code is saved as "Langemead12Test.py" w/ lines as: !C:\Users\Bones\Anaconda3\python.exe [1]def readFastq(SRR835775_1.first1000.fastq) Red Error underline def [pylint] E0001:invalid syntax (, line…
Triage
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Explanation of a code about lineIndex , to collect reads from a file

Here the aim is to build a graph from a collection of stings (reads) in a FASTQ file. But first, we implement the following function that gets the reads. We remove the new line character from the end of each line (with str.strip()), and for…
s4swe natraj
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Bash Conditional IF statement after string within FASTQ header

I would like to extract only reads that have a coverage above 2 and length above 504. This is all stored in each header of FASTQ file. However I can't workout a one-liner that would filter based on these qualities. See an example of what two of the…
bio_bob_blob
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