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,
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.