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Old 05-23-2014, 03:48 AM   #41
WhatsOEver
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Location: Germany

Join Date: Apr 2012
Posts: 215
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Dear Brian,

I have some questions about the optional fields (TAG:TYPE:VALUE stuff) that can be added in the SAM file by bbmap. Take the following multiple-mapped read as example

Quote:
readNameHere 16 chr11 106018977 55 6M3I17M * 0 0 GCTTTGAAAAATTTTCTGCATGCCCA /4122:...00....=<<<=<<4449 XT:A:R NM:i:5 AM:i:55 XM:i:2 NH:i:20
readNameHere 272 chrX 119093161 50 18M5I3M * 0 0 * * NM:i:6 AM:i:50 XM:i:2 NH:i:20
readNameHere 272 chrX 45789727 49 1M3I22M * 0 0 * * NM:i:6 AM:i:49 XM:i:2 NH:i:20
readNameHere 272 chr20 23542459 49 18M5I3M * 0 0 * * NM:i:6 AM:i:49 XM:i:2 NH:i:20
readNameHere 256 chr3 151169846 47 1M3I3M3I16M * 0 0 * * NM:i:6 AM:i:47 XM:i:2 NH:i:20
readNameHere 256 chr4 27414930 47 1M1I5M12N17M1I1M * 0 0 * * NM:i:2 AM:i:47 XM:i:2 XS:A:+ NH:i:20
readNameHere 272 chrX 89494814 46 26M * 0 0 * * NM:i:8 AM:i:46 XM:i:2 NH:i:20
readNameHere 272 chrY 3677157 46 26M * 0 0 * * NM:i:8 AM:i:46 XM:i:2 NH:i:20
readNameHere 272 chr12 126969193 46 4M2D22M * 0 0 * * NM:i:6 AM:i:46 XM:i:2 NH:i:20
readNameHere 256 chr21 31585993 45 5M1I20M * 0 0 * * NM:i:5 AM:i:45 XM:i:2 NH:i:20
readNameHere 256 chr5 80894028 45 7M1I18M * 0 0 * * NM:i:6 AM:i:45 XM:i:2 NH:i:20
readNameHere 272 chr6 85600169 45 26M * 0 0 * * NM:i:7 AM:i:45 XM:i:2 NH:i:20
readNameHere 272 chr9 81596079 44 18M1I7M * 0 0 * * NM:i:6 AM:i:44 XM:i:2 NH:i:20
readNameHere 256 chr3 170762912 43 1M3I22M * 0 0 * * NM:i:7 AM:i:43 XM:i:2 NH:i:20
readNameHere 256 chr13 20507692 42 26M * 0 0 * * NM:i:6 AM:i:42 XM:i:2 NH:i:20
readNameHere 256 chr12 28169470 42 5M2I19M * 0 0 * * NM:i:6 AM:i:42 XM:i:2 NH:i:20
readNameHere 256 chr7 42988607 41 26M * 0 0 * * NM:i:7 AM:i:41 XM:i:2 NH:i:20
readNameHere 256 chr3 103868859 41 26M * 0 0 * * NM:i:8 AM:i:41 XM:i:2 NH:i:20
readNameHere 272 chrX 45152661 40 26M * 0 0 * * NM:i:7 AM:i:40 XM:i:2 NH:i:20
readNameHere 272 chr18 60932877 39 26M * 0 0 * * NM:i:8 AM:i:39 XM:i:2 NH:i:20
Concerning XM: From the readme it says "Indicates number of best alignments". But what are these exactly? I expected all 26M from my example to be best alignments?! Or does it mean that there are mismatches in some of these alignments which I don't see as I didn't change the samversion parameter to 1.4 (btw: I have samtools 0.1.19 installed. This is able to handle '=' and 'X', isn't it?)

Concerning XS: I run bbmap using -xstag=unstranded as I read it somewhere in this thread and I want to use cufflinks afterwards. I thought that the '+' and '-' as values refer to the strand in this field and I also have '+' and '-' values set in different reads. If this is true, where is the difference to -xstag=true?

Concerning YS: This stores the end position of a read? So its pos + the alignment length of the read?

Concerning YI: The identity is simple the number of (mismatches + indels) / read-length?


Thanks a lot in advance for your help and this amazing amount of possibilities !
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