search

aryeelab / guideseq

Analysis pipeline for the GUIDE-seq assay.
GNU Affero General Public License v3.0
76 stars 53 forks source link

Missing index files #60

Open nechamaklt11 opened 4 years ago

nechamaklt11 commented 4 years ago

Hi, I have undemultiplexed fastq files that i'd like to analyze using guideseq, but unfortunataly I don't have the two index files (I didn't change the miseq settings before the run). Is there any way i can use guideseq without having the index files?

thanks in advance

matandro commented 3 years ago

You can reuse blc2fastq on your BCL files with the flag. it will re demultiplex and give you the index files. You can also put a fake index in the sample sheet to get an "undetermined" file and run the entire process with guideseq.

If you want to do the "start" by yourself you can get to post umi taggin (question is how do you pull the umi if you have the same design where it sits in index2) After umi tagging your read labels (lines that starts with @) should end with <umi>_<first 6 letters of R1>_<first 6 letters of R2>. If you can get to that point by yourself you can run alignment and such by yourself. If you have no UMI you can probably do some long random sequence instead of the UMI part or try to run it without consolidating (I haven't tried but it might work)