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<DIV>Thanks for reply.</DIV>
<DIV> </DIV>
<DIV>Best</DIV>
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<DIV><B>From:</B> <A href="mailto:yarden@mit.edu">Yarden Katz</A></DIV>
<DIV><B>Date:</B> 2013-08-07 10:43</DIV>
<DIV><B>To:</B> <A href="mailto:yu_peng@126.com">yu_peng</A></DIV>
<DIV><B>CC:</B> <A href="mailto:miso-users@mit.edu">miso-users</A></DIV>
<DIV><B>Subject:</B> Re: [miso-users] Problem of overhang-len
(misopy-0.4.9)</DIV></DIV></DIV>
<DIV>
<DIV>Hi,</DIV>
<DIV> </DIV>
<DIV>That is correct; overhang is forced to be 1 in light of our new single-end algorithm which is considerably more efficient, but won't handle overhangs for now (future releases will hopefully address this.) You could preprocess your BAM to only keep reads that meet your overhang criteria.</DIV>
<DIV> </DIV>
<DIV> --Yarden</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>On Aug 6, 2013, at 9:52 PM, yu_peng wrote:</DIV>
<DIV> </DIV>
<DIV>> Hi,colleagues:</DIV>
<DIV>> </DIV>
<DIV>> I am using misopy-0.4.9 in single-end mode with --overhang-len 4, however the background process shows that</DIV>
<DIV>> misopy still use --overhang-len 1, is it right?</DIV>
<DIV>> </DIV>
<DIV>> /usr/bin/python2.7 /home/yup/lib64/python2.7/site-packages/misopy/run_miso.py --compute-genes-from-file 1CF3_SE/batch-genes/batch-3_genes.txt 1CF3.uniq_bam 1CF3_SE --read-len 101 --overhang-len 1 --settings-filena</DIV>
<DIV>> me /home/yup/lib64/python2.7/site-packages/misopy/settings/miso_settings.txt</DIV>
<DIV>> </DIV>
<DIV>> </DIV>
<DIV>> </DIV>
<DIV>> ***************************************</DIV>
<DIV>> Peng Yu, Ph.D.</DIV>
<DIV>> Institute of Molecular Medicine</DIV>
<DIV>> Room 303, Yingjie Center</DIV>
<DIV>> Peking University</DIV>
<DIV>> Beijing 100871, China</DIV>
<DIV>> ****************************************</DIV>
<DIV>> _______________________________________________</DIV>
<DIV>> miso-users mailing list</DIV>
<DIV>> miso-users@mit.edu</DIV>
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