User: steve

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steve2.4k
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Posts by steve

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Comment: C: Automatic IGV snapshot script
... The usage of .bam files or any other format is entirely dependent on IGV. Have you tried using it with .tdf files? Let me know if it doesn't work. Though if it does not work, you would have to investigate the IGV batch script commands needed to use them, since this tool is really just a wrapper arou ...
written 6 days ago by steve2.4k
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Comment: C: Automatic IGV snapshot script
... Yes it means that you do not have the program `xvfb-run` installed on your system. It is a wrapper script that often comes bundled with your server X11 installation. Unfortunately I am not sure that I can provide a copy because from what I've seen it can be a little platform specific. For this reaso ...
written 11 days ago by steve2.4k
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Comment: C: GPU based parallel processing in genomics tools
... In addition to this, much older software that is able to utilize CPU multithreading reaches peak throughput at 8-12 CPU threads, with diminishing returns after that. So if your workload is small, you might not even see much increase in performance with more CPUs. Unless you start moving into running ...
written 27 days ago by steve2.4k
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Comment: C: Create Chromosome Ideogram w/ out reference genome
... you can just make the plots yourself custom if you know all the coordinates and chrom sizes you want to use; some guidelines for doing a custom ideogram/karyotype are here: https://www.biostars.org/p/269857/ ...
written 27 days ago by steve2.4k
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Comment: C: What Does Samtools Flagstat Results Mean?
... Would you be able to match your descriptions of these variables with the actual samtools flagstat output shown in the original post? Despite your thorough writeup, I still cannot clearly figure out what any of the numbers are supposed to mean. The C code is not readable at all so the variable names ...
written 4 weeks ago by steve2.4k
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Comment: C: Pararellization in GATK 4
... keep in mind that you can ask Broad personnel yourself on their forum: https://gatkforums.broadinstitute.org/gatk/categories/ask-the-team ...
written 5 weeks ago by steve2.4k
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Comment: C: How rare are somatic mutations?
... depends completely on your variant calling methods and your variant filtering methods. You could call hundreds or thousands of variants on a sample but then filter down to single digit final variant list to use for TMB. Or anything in between. ...
written 5 weeks ago by steve2.4k
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Comment: C: Visualizing & plotting variant reads within BAM files programmatically?
... there is script for this here: https://github.com/stevekm/IGV-snapshot-automator ...
written 6 weeks ago by steve2.4k
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Answer: A: Is it possible to run IGV in batch mode without opening the GUI?
... Yes. Check out the script here, which can create and run your IGV snapshots on a .bam file with a .bed file as target regions to snapshot: https://github.com/stevekm/IGV-snapshot-automator It uses xvfb in an automated fashion as described by Pierre. If you just want the CLI command to use, it wou ...
written 6 weeks ago by steve2.4k
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Comment: C: Error when trying to run IGV on server
... I am guessing that 1.7 is based on Java 7? If thats the case you will need to update this. ...
written 9 weeks ago by steve2.4k

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Popular Question 6 weeks ago, created a question with more than 1,000 views. For HOMER motif discovery gives inconsistent results on repeated runs
Scholar 12 weeks ago, created an answer that has been accepted. For A: HOMER mergePeaks totals don't add up to peaks input
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
Appreciated 3 months ago, created a post with more than 5 votes. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
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Great Question 6 months ago, created a question with more than 5,000 views. For How to tell which transcript is the canonical transcript?
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Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
Great Question 9 months ago, created a question with more than 5,000 views. For Creating chromosome karyotype plot with R and ggplot2
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Popular Question 21 months ago, created a question with more than 1,000 views. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Scholar 21 months ago, created an answer that has been accepted. For A: HOMER mergePeaks totals don't add up to peaks input
Popular Question 22 months ago, created a question with more than 1,000 views. For How to tell which transcript is the canonical transcript?
Popular Question 23 months ago, created a question with more than 1,000 views. For How to tell which transcript is the canonical transcript?

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