How do I find out the read lenght of a fastq file?
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3.8 years ago
sandKings ▴ 40

I'm sorry for asking such a lame question but I have several RNA-Seq datasets and none of the papers have specified the read length of the fastq files. I use STAR for alignment so I need to have a corresponding STAR index of correct read length. Is there a tool that can detect this for us? Thanks!

RNA-Seq • 9.5k views
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3.8 years ago

How do I find out the read lenght of a fastq file?

if this is what you are asking then

seqkit fx2tab -nl <your.fastq.file>

You can find seqkit here

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I think it worked.

It returned a series of lines in this format.

SRR9108806.4388388 4388388/1    75
SRR9108806.4388389 4388389/1    75

Does that mean my fastq file is 75bp read?

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Yes, here is the excerpt from the help section

convert FASTA/Q to tabular format, and provide various information,
like sequence length, GC content/GC skew.

Usage:
  seqkit fx2tab [flags]

Flags:
  -a, --alphabet               print alphabet letters
  -q, --avg-qual               print average quality of a read
  -B, --base-content strings   print base content. (case ignored, multiple values supported) e.g. -B AT -B N
  -I, --case-sensitive         calculate case sensitive base content
  -g, --gc                     print GC content
  -G, --gc-skew                print GC-Skew
  -H, --header-line            print header line
  -h, --help                   help for fx2tab
  -l, --length                 print sequence length
  -n, --name                   only print names (no sequences and qualities)
  -i, --only-id                print ID instead of full head
  -b, --qual-ascii-base int    ASCII BASE, 33 for Phred+33 (default 33)
  -s, --seq-hash               print hash of sequence (case sensitive)
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3.8 years ago

seqkit stats -a input.fq/fastq.(gz) should give you the possible basic stats about fastq file. Quick one liner would be:

awk 'NR%4==2 {print length}' input.fastq | sort -n | uniq -c | sort -rh | head -1. First column (with number) read number and second column (with number) read length.

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