[galaxy-dev] CAGE data - trimming SAM files (functionality suggestion)

Hello,

I work sometimes with galaxy analysing of short reads but actually I very much lack the function of keeping only first nucleotide of the read in SAM file. This is not so straightforward to do, I need to modifiy sequence, quality scores and CIGAR. It would be very useful for looking e.g on CAGE (cap analysis of gene expression) data where only 5' most of the read indicates end of mRNA molecule and rest of the read is needed only to map it to its location, then is unnecessary.

Hope it can be easily implemented Best, Lukasz