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Hello there,
I am confusing about the nubmber of reads prep_reads program game me in tophat run.
for example, I counted my reads in fastq file by wc -l and devided it by 4,
then I got 43744119.
But after running tophat, i found out that the number of reads in
prep_reads.info was different than original one.
cat prep_reads.info
left_min_read_len=12
left_max_read_len=91
left_reads_in =43661221
left_reads_out=43388544
right_min_read_len=12
right_max_read_len=91
right_reads_in =43661221
right_reads_out=43434368
why does it occur?? tophat does something before prep_reads and filtered out some reads ??
FYI, there have been no discrepancy at least in tophat 1.3.2.
I think this occurs after tophat2 ....
I would appreciate any your help!!
zun
I am confusing about the nubmber of reads prep_reads program game me in tophat run.
for example, I counted my reads in fastq file by wc -l and devided it by 4,
then I got 43744119.
But after running tophat, i found out that the number of reads in
prep_reads.info was different than original one.
cat prep_reads.info
left_min_read_len=12
left_max_read_len=91
left_reads_in =43661221
left_reads_out=43388544
right_min_read_len=12
right_max_read_len=91
right_reads_in =43661221
right_reads_out=43434368
why does it occur?? tophat does something before prep_reads and filtered out some reads ??
FYI, there have been no discrepancy at least in tophat 1.3.2.
I think this occurs after tophat2 ....
I would appreciate any your help!!
zun
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