User: RoseString

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RoseString0
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Posts by RoseString

<prev • 11 results • page 1 of 2 • next >
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Is HISAT2 able to output only the best alignment?
... I am studying a repetitive region in which multiple lncRNAs are transcribed. For now, I am following the HISAT2-StringTie pipeline to assemble and quantify novel lncRNAs from this region. Because of the repetitive nature of this region, I only want to keep reads that are 1. not strictly uniquely m ...
hisat2 written 5 months ago by RoseString0 • updated 4 months ago by prasundutta87310
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Comment: C: Reading single-end reads takes forever
... **UPDATE:** The run has been successfully finished when I switched to Open MPI 2.1.0. Thanks! ...
written 22 months ago by RoseString0
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Comment: C: Reading single-end reads takes forever
... Hi @benv, I added v=-v to my command and found that the reading step became really slow when it reached ~30%. I read a post that had a similar problem [http://seqanswers.com/forums/showthread.php?t=61602][1] and followed it to switch from **openmpi** to **mpich3**. The speed did improve significant ...
written 22 months ago by RoseString0
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Comment: C: Reading single-end reads takes forever
... Thank you so much for your detailed instruction, @benv. That's really helpful! I'm gonna try your suggested commands. ...
written 22 months ago by RoseString0
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Reading single-end reads takes forever
... Dear Abyss developers, **Background**: I recently had success in using Abyss 2.0.2 to assemble my SE (25x), PE (25x) and MP (50x) reads into an assembly with scaffold N50 of 2Mb, which is relatively good. However, the unitig N50 is only 4 Kb, so lots of Ns are present in the sequences. It seems tha ...
abyss written 22 months ago by RoseString0 • updated 22 months ago by benv710
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Comment: C: Abyss-map complains 'missing arguments'
... It works! Thank you! ...
written 22 months ago by RoseString0
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Comment: C: Abyss-map complains 'missing arguments'
... Actually it's the command `abyss-map -j16 -l40 SWS-3.fa` that complains 'missing argument'. I checked abyss-map --help, and `abyss-map [OPTION]... QUERY... TARGET` needs both query and target, but the command generated by abyss only has one argument? ...
written 22 months ago by RoseString0
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Abyss-map complains 'missing arguments'
... I am running the latest Abyss 2.0.2. My command line is: abyss-pe np=16 name=SWS k=70 lib='pe' mp='mp1 mp2 mp3 mp4' \ se='SWS_SE.trimmomatic.fq.gz' \ pe='SWS_PE_1.trimmomatic.fq.gz SWS_PE_2.trimmomatic.fq.gz' \ mp1='SWS_MP_1-4Kb_1.trimmomatic.fq.gz SWS_MP_1-4Kb_2.trimmomatic.fq.gz' ...
abyss written 22 months ago by RoseString0 • updated 22 months ago by benv710
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Comment: C: How to calculate Tajima's D and Fay & Wu's H for unphased data?
... Just an update. I found a [study][1] using your method. They call this process 'haploidize data'. [1]: http://www.nature.com/nature/journal/v491/n7426/full/nature11584.html ...
written 3.0 years ago by RoseString0
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Comment: C: How to calculate Tajima's D and Fay & Wu's H for unphased data?
... Thanks! Do you know any literature doing the random assignment of variants if the data is unphased? ...
written 3.0 years ago by RoseString0

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Popular Question 21 months ago, created a question with more than 1,000 views. For How to calculate Tajima's D and Fay & Wu's H for unphased data?

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