Hi, I used FASTP but it appears that it does not create tag count. On the other hand, preprocess.seq is able to produce it.
It appears that tag-count format is normalized and has the following format:
$ head 2600_norm.txt
==> 2600_norm.txt <==
AAAAAAAAAAAAAAAAAAA 1
AAAAAAAAAAAAAAAAAAAAAA 1
AAAAAAAAAAAAAAAAAAAAAAA 1
AAAAAAAAAAAAAAAAAAAAAAAA 2
AAAAAAAAAAAAAAAAAAAAAAAAAA 1
AAAAAAAAAAAAAAAACTTGCGGCC 1
AAAAAAAAAAAAAAAATGTCTGGACA 1
AAAAAAAAAAAAAAACCCTAGCCT 1
AAAAAAAAAAAAAAATCAATGGCGTA 1
AAAAAAAAAAAAAAATCGCGGCC 1
Is there a way to create tag count from FASTP results?
Thank you in advance,
If those are simple counts of sequences then you could generate them by using reformat.sh from BBMap suite :
reformat.sh in=your.fq out=stdout.fa | grep -v "^>" | sort | uniq -c > sequence_count
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We don't normally use the word "tag" in this context anymore (that hasn't been used much in the past ~8 years). What is your end goal with this? For what it's worth, fastp is meant for read trimming and QC, nothing else.
I want to use PHASIS, and one of the supported formats is a tag-count. However, it was not working with the FASTA file, but I heard that it worked with tag-count.
It's unfortunate that they don't document what "tag-count" format is, since it's not something commonly used or that I've even heard of.
I found the tag-count files here and it appears that they did sort normalization. However, I do not how to create this file.