User: Jee2

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Jee220
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Posts by Jee2

<prev • 12 results • page 1 of 2 • next >
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How to plot the output of bedtools genomecov as a histogram using gnuplot?
... I have genomecov output as chr1 0 145821816 195123441 0.747331 chr1 1 28676143 195123441 0.146964 chr1 2 6883876 195123441 0.0352796 chr1 3 3340282 195123441 0.0171188 chr1 4 2296338 195123441 0.0117686 chr1 5 1775261 195123441 0.00909814 chr1 6 1423228 195123441 0.00729399 I would like to ...
genomecov histogram gnuplot written 10 weeks ago by Jee220
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Answer: C: How to sort a BAM file by read name ?
... I did following: Installed anaconda and added pysam 0.8.3 package to it. Installed suspenders in anaconda environment. And it worked finally! Thanks a lot for your help. ...
written 18 months ago by Jee220
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Comment: C: How to sort a BAM file by read name ?
... Yes, it turned out that I have missed stuff during installation. I thought I did not have to install pysam separately as it was already a part of suspenders package. But I see two different versions in there pysam-0.11-py2.7-linux-x86_64.egg pysam-0.7.6-py2.7-linux-x86_64.egg But the suspender ...
written 18 months ago by Jee220
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Comment: C: How to sort a BAM file by read name ?
... I have tried running their test lapels output files as input files for suspenders and got same errors. ...
written 18 months ago by Jee220
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Comment: C: How to sort a BAM file by read name ?
... I have installed this software locally & no one else around has ever dealt with this pipeline - now looking into the installation. Thanks Adding -t argument to the pysuspender command gives traceback error ( in addition to the original SO tag error): File "/home/local_dir/suspenders-0.2.5 py ...
written 18 months ago by Jee220
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Comment: C: How to sort a BAM file by read name ?
... Yes, It has been successfully used by other groups (PMID: 27999113, 27933528) apart from the team (PMID 27933528) that came up with it. I have emailed authors couple days ago and as of this writing waiting for the response. It is explicitly stated in the pipeline that for suspenders to work succe ...
written 18 months ago by Jee220
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Comment: C: How to sort a BAM file by read name ?
... I second you in that I should not need to use samtools. Indeed, samtools view -H shows that the Input.bam (output BAM file from lapels ) is already sorted by queryname. But since I get an empty suspenders output file along with the warning message, I will have to get rid of the warning message so ...
written 18 months ago by Jee220
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Comment: C: How to sort a BAM file by read name ?
... I have pylapels -n -o lapels/Mat.bam WSBEiJ_b38_f.mod WSBalign /accepted_hits.bam ...
written 18 months ago by Jee220
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Comment: C: How to sort a BAM file by read name ?
... Yes, I used lapels with -n pylapels -n -o lapels/Mat.bam WSBEiJ_b38_f.mod WSBalign /accepted_hits.bam Thanks for your comment on indexing. I will remove its mention from my question as my requirement is just getting the Bam file sorted by query_name ...
written 18 months ago by Jee220
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Comment: C: How to sort a BAM file by read name ?
... I am following [the pipeline][1] you mentioned and it actually uses pylapels. Thanks, I will give 1.4 a try. [1]: https://github.com/holtjma/suspenders/wiki/Lapels-and-Suspenders-Pipeline ...
written 18 months ago by Jee220

Latest awards to Jee2

Popular Question 17 months ago, created a question with more than 1,000 views. For How to sort a BAM file by read name ?
Scholar 18 months ago, created an answer that has been accepted. For C: How to sort a BAM file by read name ?
Teacher 18 months ago, created an answer with at least 3 up-votes. For C: How to sort a BAM file by read name ?

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