RNA Seq

Question

[far.zi]

I have a fasta file and I need to count the number of exact matched sequences in it. I tried

cat my.fasta | tr -d "\n" | grep "MySequence"

but it's not working for me.

[Ram]

How is this question related to RNAseq?

[seidel]

How is it not working for you? Does grep not find the pattern that you can see is there? Do you need to create 1 line per fasta entry? (Multiline Fasta To Single Line Fasta)? If you have bowtie available, you could create an alignment index with your fasta, then supply "MySequence" on the command line, and count up the results.

Answer 1

[swbarnes2]

I'd do

grep ">" myfile.fa | wc -l

That should just count the number of lines with ">", so line breaks won't matter.

[Ram]

Going off the grep in their command and the phrase "exact sequence" in their post, I think OP is trying to count number of exact matches to their query sequence.

[far.zi]

Yes, you're right. I need to count how many of an exact short sequence are there in my data. I could open it in TextWrangler and find but the file is huge and my mac is not helping.

[Ram]

Please edit your question and rephrase it so this is clear to everyone reading the question. This question has also been addressed multiple times on the forum, please use the search bar. If you want a quick lead, try exploring seqkit grep.