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
Lukasz J. Kielpinski
PhD student

Department of Biology, University of Copenhagen
RNA Biology Group
Ole Maal√łes Vej 5, room 3.1.17
2200 Copenhagen N

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