I ran tophat version 1.3.2 to align my deep sequencing data to my reference genome via the following command
tophat --solexa1.3-quals –p 6 –o /control/8905X1/tophat /rice_index/rice_index /8905X1/8905X1.txt
It generated a file called accepted_hits.bam.
I converted the file to a bed file using the bamToBed tool.
Then split the file up based on chromosomes. Here are the results:
331723028 May 11 09:26 accepted_hits_bed_Chr1
119325730 May 11 09:26 accepted_hits_bed_Chr10
123994839 May 11 09:26 accepted_hits_bed_Chr11
121898474 May 11 09:27 accepted_hits_bed_Chr12
416137943 May 11 09:27 accepted_hits_bed_Chr2
334052893 May 11 09:27 accepted_hits_bed_Chr3
161529836 May 11 09:27 accepted_hits_bed_Chr4
347228298 May 11 09:28 accepted_hits_bed_Chr5
189465060 May 11 09:28 accepted_hits_bed_Chr6
200695493 May 11 09:28 accepted_hits_bed_Chr7
171194241 May 11 09:28 accepted_hits_bed_Chr8
759976461 May 11 09:29 accepted_hits_bed_Chr9
2184791 May 11 09:29 accepted_hits_bed_ChrSy
539606 May 11 09:29 accepted_hits_bed_ChrUn
Tophat overloaded chromosome 9 which is one of the smaller chromosomes.
Unless this can be resolved, I recommend not using Tophat.
tophat --solexa1.3-quals –p 6 –o /control/8905X1/tophat /rice_index/rice_index /8905X1/8905X1.txt
It generated a file called accepted_hits.bam.
I converted the file to a bed file using the bamToBed tool.
Then split the file up based on chromosomes. Here are the results:
331723028 May 11 09:26 accepted_hits_bed_Chr1
119325730 May 11 09:26 accepted_hits_bed_Chr10
123994839 May 11 09:26 accepted_hits_bed_Chr11
121898474 May 11 09:27 accepted_hits_bed_Chr12
416137943 May 11 09:27 accepted_hits_bed_Chr2
334052893 May 11 09:27 accepted_hits_bed_Chr3
161529836 May 11 09:27 accepted_hits_bed_Chr4
347228298 May 11 09:28 accepted_hits_bed_Chr5
189465060 May 11 09:28 accepted_hits_bed_Chr6
200695493 May 11 09:28 accepted_hits_bed_Chr7
171194241 May 11 09:28 accepted_hits_bed_Chr8
759976461 May 11 09:29 accepted_hits_bed_Chr9
2184791 May 11 09:29 accepted_hits_bed_ChrSy
539606 May 11 09:29 accepted_hits_bed_ChrUn
Tophat overloaded chromosome 9 which is one of the smaller chromosomes.
Unless this can be resolved, I recommend not using Tophat.
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