Hi everyone,
MRNM is the 7th field in the sam file. I got the sam output from tophat, it seems that the MRNM is not correct in my case.
$ grep "HWI-EAS244_1_1_116_848_845_0_1_12496949" accepted_hits.sam
HWI-EAS244_1_1_116_848_845_0_1_12496949;2 163 chr1 14628 255 75M = 14859 0 CCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTGGGTCTGGGGGGGCAGGTGTCATGGAGCCCCCTACGCT ABA?BBBB=A>BABA@2@B=;;=9<AB8ABB38=0>A?<=4AA<9??=########################### NM:i:2
HWI-EAS244_1_1_116_848_845_0_1_12496949;1 83 chr9 14859 255 76M = 14628 0 GGCAAAGGAGGGATGGAGTCTGACACGCGGACAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAG 7>@@)@B=1@B;<(8@?@@9@A>B@BBABAAA@AAAB@@A@<AABABBBA?BB@BBBBB@BABCBCCCCCCCCCCB NM:i:0
The MRNM is '=' here, but one is on chr1 and another is on chr9.
From the manual , if MRNM is '=', the mate pairs should be on the same reference(same chromosome), but here it's on different chromosome. Does anybody meet the same problem? How to solve this problem?
version of tophat: tophat1.0.13
part of the shell code for tophat running is:
"
tophat -r 200 --mate-std-dev 200 -a 8 -m 0 -I 1000000 -p 4 -g 100 -o $OUTDIR/ --solexa1.3-quals --coverage-search --microexon-search --max-segment-intron 1000000 -G $GFF3 $INDEXDIR/hg19 $READDIR/s_1.fq $READDIR/s_2.fq
"
By the way, the FLAG (second field) in the .sam file is not correct in this case:
163="10100011"
83="1010011"
This means "The read is mapped in a proper pair", but they are on the different chromosome, how can they be properly paired?
MRNM is the 7th field in the sam file. I got the sam output from tophat, it seems that the MRNM is not correct in my case.
$ grep "HWI-EAS244_1_1_116_848_845_0_1_12496949" accepted_hits.sam
HWI-EAS244_1_1_116_848_845_0_1_12496949;2 163 chr1 14628 255 75M = 14859 0 CCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTGGGTCTGGGGGGGCAGGTGTCATGGAGCCCCCTACGCT ABA?BBBB=A>BABA@2@B=;;=9<AB8ABB38=0>A?<=4AA<9??=########################### NM:i:2
HWI-EAS244_1_1_116_848_845_0_1_12496949;1 83 chr9 14859 255 76M = 14628 0 GGCAAAGGAGGGATGGAGTCTGACACGCGGACAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAG 7>@@)@B=1@B;<(8@?@@9@A>B@BBABAAA@AAAB@@A@<AABABBBA?BB@BBBBB@BABCBCCCCCCCCCCB NM:i:0
The MRNM is '=' here, but one is on chr1 and another is on chr9.
From the manual , if MRNM is '=', the mate pairs should be on the same reference(same chromosome), but here it's on different chromosome. Does anybody meet the same problem? How to solve this problem?
version of tophat: tophat1.0.13
part of the shell code for tophat running is:
"
tophat -r 200 --mate-std-dev 200 -a 8 -m 0 -I 1000000 -p 4 -g 100 -o $OUTDIR/ --solexa1.3-quals --coverage-search --microexon-search --max-segment-intron 1000000 -G $GFF3 $INDEXDIR/hg19 $READDIR/s_1.fq $READDIR/s_2.fq
"
By the way, the FLAG (second field) in the .sam file is not correct in this case:
163="10100011"
83="1010011"
This means "The read is mapped in a proper pair", but they are on the different chromosome, how can they be properly paired?
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