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!
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sandKings •
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
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?
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)
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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Sequence Length Distribution From A Fastq File ; Awk command for fastq read length and number of reads? ; ...