SRA extraction for SOLID data is not compatable with TopHat

Question

SRA extraction for SOLID data is not compatable with TopHat

Closed this issue 8 years ago · 1 comments

When extracting SOLID data from SRA for Tophat, need to use abi-dump not fastq-dump (see http://seqanswers.com/forums/showthread.php?t=44333) and retain quality files. Currently, following sra extraction, there is no attempt to detect whether the data is SOLID.

Propose check for SOLID data within SRA and then append correct fastqs to retain quality scores for downstream mapping.

Answer 1 · 2016-06-17T18:11:56.000Z

See 1022967.

Currently no check to make sure the downstream mapper can handle SOLID data. Should probably incorporate this at this stage in pipeline_mapping to avoid waiting for SRA extraction to complete and then working it out from the mapper log file?