Hi,
This is one of my first forays in SOLID data so please bear with me if the question is basic;
I had aligned SOLID data individually (forward, reverse) using bowtie color space -
bowtie -t -p 4 -C --sam --chunkmbs 1000 /Bowtie-Reference/Bowtie-C/h_sapiens_37_asm_c -f read1.csfasta -Q read1.QV.qual read1.sam
I ended up getting a sam file with what appears to me a malformed sam files;
1_2_1079_F3 4 * 0 0 * * 0 0 CCGTGATGGCTACCCCTGGGGTTACATATAAATT *?626A@@:@-@@@@2>>@6*5=**.;.--<@=3 XM:i:0
1_3_10_F3 0 gi|224589818|ref|NC_000006.11| 33410152 255 33M * 0 0 ATTCCCGCCTCTCCTTTCATTTGTCCACATCTC \IFIAGPMOYZL>PRAN`a/#S30FHP?J/!!' XA:i:2 MD:Z:33 NM:i:0 CM:i:4
I kind of figured that "*" on 3rd column, "@" and some CIGAR sequence in the next line as mal-formed elements. I would very much appreciate if anyone can shed some light on this and suggest any solution to this problem.
Thanks
Uma
This is one of my first forays in SOLID data so please bear with me if the question is basic;
I had aligned SOLID data individually (forward, reverse) using bowtie color space -
bowtie -t -p 4 -C --sam --chunkmbs 1000 /Bowtie-Reference/Bowtie-C/h_sapiens_37_asm_c -f read1.csfasta -Q read1.QV.qual read1.sam
I ended up getting a sam file with what appears to me a malformed sam files;
1_2_1079_F3 4 * 0 0 * * 0 0 CCGTGATGGCTACCCCTGGGGTTACATATAAATT *?626A@@:@-@@@@2>>@6*5=**.;.--<@=3 XM:i:0
1_3_10_F3 0 gi|224589818|ref|NC_000006.11| 33410152 255 33M * 0 0 ATTCCCGCCTCTCCTTTCATTTGTCCACATCTC \IFIAGPMOYZL>PRAN`a/#S30FHP?J/!!' XA:i:2 MD:Z:33 NM:i:0 CM:i:4
I kind of figured that "*" on 3rd column, "@" and some CIGAR sequence in the next line as mal-formed elements. I would very much appreciate if anyone can shed some light on this and suggest any solution to this problem.
Thanks
Uma
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