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Old 06-21-2012, 06:07 PM   #1
zun
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Location: Japan

Join Date: Oct 2010
Posts: 26
Default tophat's prep_reads gave different number of reads

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
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Old 06-26-2012, 06:49 AM   #2
giorgifm
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Location: Columbia University Medical Center

Join Date: Aug 2011
Posts: 35
Default

Dear Zun, we have the same issue, and we confirm it happens only since Tophat 2.0.0
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Old 06-26-2012, 04:43 PM   #3
zun
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Location: Japan

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Dear giorgifm

Thank you for your info
OK then I have to be careful when calculating mapping rate...

zun
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