search

Jiaxin-Fan / ASEP

8 stars 3 forks source link

Input data for ASEP #8

Open wrongbong opened 3 years ago

wrongbong commented 3 years ago

Hey, I am trying to do allele-specific expression analysis (ASE) for a few RNA seq samples ( 32 disease and 5 normal samples, unpaired unrelated). Could you suggest a pipeline/method to convert the mapped BAM files ( RNA seq) into the input format required for your tool? That wuld be really helpful. Regards,

Jiaxin-Fan commented 3 years ago

I am not an expert in data processing though. As far as I know, for raw BAM file, you should first using WASP to remove the possible allelic mapping bias (https://github.com/bmvdgeijn/WASP/tree/master/mapping). Then, call variants (samtools mpileup or GATK pipeline), annotate the position using ANNOVAR, and then summarize the reads for exonic region to a count txt file. hope that helps.

Jokendo-collab commented 4 months ago

This is a great tool but i think it will attract wider usage if you provide a clear way of preparing the input files. Is this something you plan to implement in the near future?