Hi
I got on about 6M out of 35M read mapped tophat for my sample. On doing QC I found out that there was some problem in the first 8 bases. I trimmed them and rerunning tophat (with default paramters except a mismatch of 2). I am looking at the intermediate logs and see that I still have log in which 85% of my reads fail to align.
I have two questions:
1. Can someone tell us a bit more about the intermediate files and logs generated?
2. How much does a problem in %GC content affect the alignment.
I am attaching some of the log files below:
-thanks
-LAx
______________________________________________
[liyer01@h01 logs]$ more file2vqTeB.log
# reads processed: 38843979
# reads with at least one reported alignment: 5520299 (14.21%)
# reads that failed to align: 33230242 (85.55%)
# reads with alignments suppressed due to -m: 93438 (0.24%)
Reported 8463229 alignments to 1 output stream(s)
[liyer01@h01 logs]$ more long_spanning_reads.log
long_spanning_reads v1.1.0 (1606)
--------------------------------------------
Opening S6_tophat_out/left_kept_reads.fq for reading
Opening /dev/null for reading
Opening S6_tophat_out/tmp/left_kept_reads.bwtout for reading
Loading spliced hits...done
Loading junctions...done
[liyer01@h01 logs]$ more file8W6m7g.log
# reads processed: 33230242
# reads with at least one reported alignment: 26854884 (80.81%)
# reads that failed to align: 3283599 (9.88%)
# reads with alignments suppressed due to -m: 3091759 (9.30%)
Reported 77514776 alignments to 1 output stream(s)
I got on about 6M out of 35M read mapped tophat for my sample. On doing QC I found out that there was some problem in the first 8 bases. I trimmed them and rerunning tophat (with default paramters except a mismatch of 2). I am looking at the intermediate logs and see that I still have log in which 85% of my reads fail to align.
I have two questions:
1. Can someone tell us a bit more about the intermediate files and logs generated?
2. How much does a problem in %GC content affect the alignment.
I am attaching some of the log files below:
-thanks
-LAx
______________________________________________
[liyer01@h01 logs]$ more file2vqTeB.log
# reads processed: 38843979
# reads with at least one reported alignment: 5520299 (14.21%)
# reads that failed to align: 33230242 (85.55%)
# reads with alignments suppressed due to -m: 93438 (0.24%)
Reported 8463229 alignments to 1 output stream(s)
[liyer01@h01 logs]$ more long_spanning_reads.log
long_spanning_reads v1.1.0 (1606)
--------------------------------------------
Opening S6_tophat_out/left_kept_reads.fq for reading
Opening /dev/null for reading
Opening S6_tophat_out/tmp/left_kept_reads.bwtout for reading
Loading spliced hits...done
Loading junctions...done
[liyer01@h01 logs]$ more file8W6m7g.log
# reads processed: 33230242
# reads with at least one reported alignment: 26854884 (80.81%)
# reads that failed to align: 3283599 (9.88%)
# reads with alignments suppressed due to -m: 3091759 (9.30%)
Reported 77514776 alignments to 1 output stream(s)
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