Re: [Seqan-dev] Rabema input

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

Sven,

The SAM header is optional.

I fear all fields are required. Don't despair, some can be set to constant values since we don't need paired-end mappings for Rabema.

QNAME - make sure you truncate at the first space
FLAG - only mapped/unmapped flag and strand flag are required
RNAME - make sure you truncate at the first space
POS - any output should contain this
MAPQ - ignored, set to any value
CIGAR - required for determining the alignment length
RNEXT - fix to *
PNEXT - fix to 0
TLEN - fix to 0
SEQ - required
QUAL - ignored, can be set to length(SEQ) * "!"

HTH

*m

-----Original Message-----
From: Sven Giese [mailto:sven.giese@fu-berlin.de] 
Sent: Mittwoch, 14. März 2012 11:43
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] Rabema input

Hi everyone,

I recently started using Rabema and I also want to compare some ReadMappers which do not support the .SAM format.

Could anyone tell me which columns are mandatory for the comparison so that I could reconstruct a pseudo-Sam file?

thanks in advance!

best regards
Sven Giese


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