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Hi,
A recent paired-end TopHat run on my data created SAM files with a error I have not seen before: for the two pairs, even if the best match is found on different chromosomes, field 7 in the Alignment section (MRNM) has the value "=", which should be true only if they were on the same chromosome. I am pasting an example below, where the two PE mates map to chr1 and chrX.
Has anyone encountered this before?
Thanks,
Shurjo
A recent paired-end TopHat run on my data created SAM files with a error I have not seen before: for the two pairs, even if the best match is found on different chromosomes, field 7 in the Alignment section (MRNM) has the value "=", which should be true only if they were on the same chromosome. I am pasting an example below, where the two PE mates map to chr1 and chrX.
Code:
42RFMAAXX:2:089:0997:0562 177 chr1 225935280 255 51M = 114953101 0 ATAACACTCCAATACCACTTTGTTGTCAGTGTAAACAAGGGCATATCCCGG >=?>B9@?@ABBA>B?=BAA9AB>AB9BB@B?CC@=CBBBCB?@:BA>@>B NM:i:2 42RFMAAXX:2:089:0997:0562 113 chrX 114953101 255 51M = 225935280 0 TTGACATTGTCTCTCTTTTTGACTTTCCTTTTGCCTCTGTCTCTTCCTCAC B@>?C?B?BBCBBBCB?B:AB?BBA<@BBAABABBB@CA@B@CBBC@BB?B NM:i:1
Thanks,
Shurjo