User: ra

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ra0
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Posts by ra

<prev • 7 results • page 1 of 1 • next >
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Answer: A: how to define different batches in DESeq2 in Galaxy
... Glad you found the solution. As a note, [Galaxy Biostar][1] focuses on using Galaxy. [1]: https://biostar.usegalaxy.org/ ...
written 3 months ago by ra0
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Comment: C: HTSeq-counts can not map any reads to gtf file
... Have you had a look at your .bam file in IGV? This will allow you to visualise the alignments from Bowtie and indicate if the problem lies at your mapping stage. ...
written 3 months ago by ra0
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Comment: C: Downsample a Bam file (Picard DownsampleSam)
... That's great Kevin, thanks for the link above! It's good to know that you also use `DownsampleSam` for downsampling, as opposed to the other tools I had considered. From what I can tell, this issue I am having hasn't been mentioned before by anyone else. Out of curiosity, I downsampled a .bam f ...
written 3 months ago by ra0
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Comment: C: Downsample a Bam file (Picard DownsampleSam)
... Absolutely, neither the documentation or the code are very clear in this regard. Thanks for your time Kevin, your inputs have been very helpful!! ...
written 3 months ago by ra0
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Comment: C: Downsample a Bam file (Picard DownsampleSam)
... Thanks for getting back, I appreciate your time. I completely agree with you that the documentation are not clear in stating exactly how `DownsampleSam` is handling secondary reads. I had a look at the code trail as you kindly suggested. This may be due to my lack of understanding, but it looks ...
written 3 months ago by ra0
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Comment: C: Downsample a Bam file (Picard DownsampleSam)
... Thank you for your reply and highlighting the above information from the document. Following on from this, the help information (from `picard DownsampleSam -h`) for Picard release 1.130 states: > Randomly down-sample a SAM or BAM file to retain a random subset of > the reads. Mate-pairs are ...
written 3 months ago by ra0
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Downsample a Bam file (Picard DownsampleSam)
... Hi all, I have been using Picard's `DownsampleSam` to extract random alignments from a .bam file. The tool documentation for `DownsampleSam` states that > Reads marked as not primary alignments are all discarded However, when running `DownsampleSam` (Picard release 2.4.1) on my .bam file, t ...
picard downsample rna-seq bam written 3 months ago by ra0

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Supporter 3 months ago, voted at least 25 times.

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