Fixing MGI Sequence Headers - FASTQ Format

Question

[joe_genome]

I am trying to fix the headers of the fastq data from MGI, this comes in a different format than expected Illumina data, this gives issues downstream when trying to use tools such as samtools, hisat2.

   @E250087456L2C221R00100000555#GGGTTTA/1

UMIs also come in a separate file so we need to parse this, not sure on how to approach.

Possible approach?

   @E250087456L2C221R00100000555#GGGTTTA:AATTGGCCTTAA/1

Answer 1

[GenoMax]

Give this a try: https://sagc-bioinformatics.github.io/mgikit/reformat

[joe_genome]

This worked quite well, thank you