Hello,all
I use tophat to analyze a RNA-seq data,while I find the log folder contain many log files,such as "bowtie.left_kept_reads.fixmap.log","bowtie.left_kept_reads_seg1.fixmap.log"and"bowtie.left_kept_reads_seg2.fixmpa.log"
The content of the 3 files are like this:
"bowtie.left_kept_reads.fixmap.log":
# reads processed: 12384696
# reads with at least one reported alignment: 10847735 (87.59%)
# reads that failed to align: 1448633 (11.70%)
# reads with alignments suppressed due to -m: 88328 (0.71%)
Reported 12152934 alignments to 1 output stream(s)
"bowtie.left_kept_reads_seg1.fixmap.log":
# reads processed: 1448633
# reads with at least one reported alignment: 559397 (38.62%)
# reads that failed to align: 885817 (61.15%)
# reads with alignments suppressed due to -m: 3419 (0.24%)
Reported 895982 alignments to 1 output stream(s)
"bowtie.left_kept_reads_seg2.fixmpa.log":
# reads processed: 1448633
# reads with at least one reported alignment: 545362 (37.65%)
# reads that failed to align: 897019 (61.92%)
# reads with alignments suppressed due to -m: 6252 (0.43%)
Reported 850850 alignments to 1 output stream(s)
My quetion is :What's the difference of the 3 files? And how many reads have been mapped to the genome in my analysis?
Thanks.
I use tophat to analyze a RNA-seq data,while I find the log folder contain many log files,such as "bowtie.left_kept_reads.fixmap.log","bowtie.left_kept_reads_seg1.fixmap.log"and"bowtie.left_kept_reads_seg2.fixmpa.log"
The content of the 3 files are like this:
"bowtie.left_kept_reads.fixmap.log":
# reads processed: 12384696
# reads with at least one reported alignment: 10847735 (87.59%)
# reads that failed to align: 1448633 (11.70%)
# reads with alignments suppressed due to -m: 88328 (0.71%)
Reported 12152934 alignments to 1 output stream(s)
"bowtie.left_kept_reads_seg1.fixmap.log":
# reads processed: 1448633
# reads with at least one reported alignment: 559397 (38.62%)
# reads that failed to align: 885817 (61.15%)
# reads with alignments suppressed due to -m: 3419 (0.24%)
Reported 895982 alignments to 1 output stream(s)
"bowtie.left_kept_reads_seg2.fixmpa.log":
# reads processed: 1448633
# reads with at least one reported alignment: 545362 (37.65%)
# reads that failed to align: 897019 (61.92%)
# reads with alignments suppressed due to -m: 6252 (0.43%)
Reported 850850 alignments to 1 output stream(s)
My quetion is :What's the difference of the 3 files? And how many reads have been mapped to the genome in my analysis?
Thanks.
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