User: bioinfo8

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bioinfo890
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Posts by bioinfo8

<prev • 140 results • page 1 of 14 • next >
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Comment: C: Tools To Calculate Average Coverage For A Bam File?
... @[genomax][1] My bam files are very big and `Qualimap` has not been helpful, so as `bbmap` which is Java-based (memory issues like `Picard` and `QoRTs`) and hence I used `samtools depth`. My depth files are also in GB. [1]: https://www.biostars.org/u/18713/ ...
written 1 day ago by bioinfo890
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Comment: A: Tools To Calculate Average Coverage For A Bam File?
... Hi, I have multiple paired-end bam files from RNA-Seq data, already aligned and computed depth with `samtools depth > bam.depth`. Would any one please guide for any straight forward/latest way to compute coverage plots, avg. coverage plots and other metrics from depth files? `Picard CollectRNAs ...
written 1 day ago by bioinfo890
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Comment: C: Tools To Calculate Average Coverage For A Bam File?
... @[Jorge Amigo][1] samtools depth *bamfile* | awk '{sum+=$3} END { print "Average = ",sum/NR}' by @[russdurrett][2] also gives same output for my paired-end bam file from RNA-Seq:-) [1]: https://www.biostars.org/u/375/ [2]: https://www.biostars.org/u/7480/ ...
written 1 day ago by bioinfo890
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RSeQC installation error
... Hi, I am trying to install RSeQC as per [instructions][1], but getting following error : $python setup.py install --root=$HOME/.local/bin Unable to find pgen, not compiling formal grammar. Compiling /tmp/easy_install-TF_81x/Cython-0.27.1/Cython/Plex/Scanners.py because it changed. ...
python ngs qc rseqc written 2 days ago by bioinfo890 • updated 1 day ago by h.mon9.0k
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Comment: C: Error in running QoRTs after hisat2 alignment
... @[h.mom][1] I tried with -Xmx64g, but same error. I don't want to sort bam by name as it will take so longer and I have multiple files. [1]: https://www.biostars.org/u/6093/ ...
written 2 days ago by bioinfo890
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Comment: C: Error in running QoRTs after hisat2 alignment
... @[h.mom][1] Thanks, I will try and let you know. [1]: https://www.biostars.org/u/6093/ ...
written 2 days ago by bioinfo890
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Error in running QoRTs after hisat2 alignment
... Hi, I ran [QoRTs][1] on multiple bam files and here is the log for one of them: I tried -Xmx4G, -Xmx8G, -Xmx16G, but still same errors. Please guide. Thanks. 1.sorted.bam Starting QoRTs v1.2.42 (Compiled Fri Jun 2 12:23:55 EDT 2017) Starting time: (Mon Oct 16 13:33:39 MEST 2017) ...
qorts paired-end samtools java rna-seq written 3 days ago by bioinfo890 • updated 2 days ago by h.mon9.0k
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Comment: C: Whether to use all aligned reads (QC-passed) or only properly-paired reads from
... @[James Ashmore][1]: Ok, thanks.I am planning to use Stringtie and Ballgown [1]: https://www.biostars.org/u/13632/ ...
written 3 days ago by bioinfo890
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Comment: C: Whether to use all aligned reads (QC-passed) or only properly-paired reads from
... Thanks. I have observed that using properly-paired reads will lead to more confidence in the data (for e.g. in case of exome analysis), but I want to know in case of RNA-Seq. I would not consider doing hisat2 alignment again as it is so much time-consuming. I used Kallisto, Sleuth approach, but I ...
written 3 days ago by bioinfo890
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Comment: C: Whether to use all aligned reads (QC-passed) or only properly-paired reads from
... I am already done with hisat2 alignment for my all samples (so many) and the ultimate aim of RNA-seq is to study the differential expression of genes between different samples. Therefore, considering that I asked the question. ...
written 3 days ago by bioinfo890

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Voter 8 weeks ago, voted more than 100 times.
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Supporter 5 months ago, voted at least 25 times.

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