Consider option to add spike-in genome for calculation of bisulfite conversion rate

BIMSBbioinfo / pigx_bsseq

bisulfite sequencing pipeline from fastq to methylation reports

https://bioinformatics.mdc-berlin.de/pigx/

GNU General Public License v3.0

9 stars 4 forks source link

Open alexg9010 opened 2 years ago

alexg9010 commented 2 years ago

I guess there are multiple options how this could be achieved:

add extra spike-in genome fasta file and perform extra round of mapping
add spike-in genome sequences to main genome file and filter out after mapping which reads mapped to spike-in chromosomes
tell users to create another settings file and perform another run