Hi everyone,
I tried to find the reason for a long time. But couldn't solve my problem.
When loading my sorted bam file (with bai file in the same folder) on IGV, I could see nothing.
My bam file data looks like this:
HWI-ST261:6:66:13462:17077#TAGCTT 83 chr01 148 255 95M = 94 -149 TGTAGTTCAAAAAATTAAAGTATGTATTCAATAGAGCTGAGGAAATTGTTCATGGAGGAATGATAGTGCTTATTACACCATTTTCAAGTTATGTA EE?D@EEBDE?DHHCHFHFFDB>HEE>EEEDDHDBHDDDHEFEFHEEHEHFHHHHHHHHHHHHHFEEEEFFHFFDDEHHHFHHHHHHHHHHFHHH XA:i:0 MD:Z:8T86 NM:i:0
I tried with a bam file downloaded online. It worked when I loaded the file on IGV.
IL7_1788:1:61:1161:1010 99 MAL1 17 0 6H48M = 548 584 ACCCTGAACCCTAAACCCTAAACCCTGAACCCTAAACCCTGAACCCTG>>>>>>>>>>>>>>>>>>>>>>>><<<<<666626666666+66/662 AS:i:48 MS:i:11
My DNA-seq data is very big. My bam file was produced by galaxy. I used the steps as follows in galaxy:
map with bowtie
filter sam
sam to bam
Any suggestions will be very appreciated!
I tried to find the reason for a long time. But couldn't solve my problem.
When loading my sorted bam file (with bai file in the same folder) on IGV, I could see nothing.
My bam file data looks like this:
HWI-ST261:6:66:13462:17077#TAGCTT 83 chr01 148 255 95M = 94 -149 TGTAGTTCAAAAAATTAAAGTATGTATTCAATAGAGCTGAGGAAATTGTTCATGGAGGAATGATAGTGCTTATTACACCATTTTCAAGTTATGTA EE?D@EEBDE?DHHCHFHFFDB>HEE>EEEDDHDBHDDDHEFEFHEEHEHFHHHHHHHHHHHHHFEEEEFFHFFDDEHHHFHHHHHHHHHHFHHH XA:i:0 MD:Z:8T86 NM:i:0
I tried with a bam file downloaded online. It worked when I loaded the file on IGV.
IL7_1788:1:61:1161:1010 99 MAL1 17 0 6H48M = 548 584 ACCCTGAACCCTAAACCCTAAACCCTGAACCCTAAACCCTGAACCCTG>>>>>>>>>>>>>>>>>>>>>>>><<<<<666626666666+66/662 AS:i:48 MS:i:11
My DNA-seq data is very big. My bam file was produced by galaxy. I used the steps as follows in galaxy:
map with bowtie
filter sam
sam to bam
Any suggestions will be very appreciated!
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