hi,we have conducted RNA_seq mapping and alignment by tophat. Before tophat finished,we monitored the logs for bowtie ,it shows a mapping ratio as below:
# reads processed: 20788750
# reads with at least one reported alignment: 6392838 (30.75%)
# reads that failed to align: 14247986 (68.54%)
# reads with alignments suppressed due to -m: 147926 (0.71%)
Reported 14363386 alignments to 1 output stream(s)
however,after tophat finished, we rechecked the logs for bowie, the ratio of reads involved in alignment dramatically declined to a very low level:
reads processed: 20814986
# reads with at least one reported alignment: 862668 (4.14%)
# reads that failed to align: 19946494 (95.83%)
# reads with alignments suppressed due to -m: 5824 (0.03%)
Reported 1347297 alignments to 1 output stream(s)
it seems that some of our alignments have been filtered out,
could anyone tell us what happened with our alignments?
# reads processed: 20788750
# reads with at least one reported alignment: 6392838 (30.75%)
# reads that failed to align: 14247986 (68.54%)
# reads with alignments suppressed due to -m: 147926 (0.71%)
Reported 14363386 alignments to 1 output stream(s)
however,after tophat finished, we rechecked the logs for bowie, the ratio of reads involved in alignment dramatically declined to a very low level:
reads processed: 20814986
# reads with at least one reported alignment: 862668 (4.14%)
# reads that failed to align: 19946494 (95.83%)
# reads with alignments suppressed due to -m: 5824 (0.03%)
Reported 1347297 alignments to 1 output stream(s)
it seems that some of our alignments have been filtered out,
could anyone tell us what happened with our alignments?
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