grep sequence larger than read length in fastq
Apologies for the naive question, if the length of each read in my fastq file is 75bp
For example something like this:
@HS25_123:4:1567:891011:23248/2
CTCCGACAGACTGAGTCGCCCGGGGGGATCTCGAGCGGCCGCCACTGTGCTGGATAATTCGAGCTCGCCCCGACG
+
CCBCCGGGGGGGGGGGGGGGFGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
is it possible to grep search for a sequence longer than 75bp?
I would assume not, but just wanted to make sure.
Thank you!
2 answers
It is possible to search but you won't get any results.
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link
written
by
Mensur Dlakic
Counting sequences >= 76 bp with seqkit seq.
seqkit seq -m 76 reads_1.fq.gz | seqkit stats
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link
written
by
shenwei356
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If that is true/known then as @Mensur said you will not get any results since no read in your will will be longer then 75 bp.
If you want to test if that statement is true, then use @shenwei's code to get an answer.
You will want to use a tool that understands fastq format rather than
grep.