User: Dave Carlson
Dave Carlson • 120
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- Stony Brook University, NY
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Posts by Dave Carlson
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... Can you check while FastQC is running whether or not the expected output files are being produced? If so, the problem is most likely that FastQC is giving the output files names (or paths) that differ from what Snakemake is expecting.
...
written 5 days ago by
Dave Carlson • 120
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... Assuming for the moment that you do want to filter based on ExcessHet, then yes that sound about right to me.
Here is some more information from the Broad that might be helpful:
https://gatkforums.broadinstitute.org/gatk/discussion/23216/how-to-filter-variants-either-with-vqsr-or-by-hard-filtering ...
written 5 days ago by
Dave Carlson • 120
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... Just checked a vcf file and the header indicates that the ExcessHet field is the
> Phred-scaled p-value for exact test of excess heterozygosity
This VCF was created using GATK's HaplotypeCaller, so you can find more information about the ExcessHet statistic [here][1].
Since the ExcessHet scor ...
written 6 days ago by
Dave Carlson • 120
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... > Do you know why this was done? Why would you collapse the "fully contained shorter coding sequences" of the GTF file and exlude the non-coding regions?
Not knowing the aims of the study in question, it's hard to say for sure. Presumably they were only interested in analyzing coding regions. ...
written 7 days ago by
Dave Carlson • 120
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... Usually, each fasta assembly will be released with its own set of annotations (in GTF of GFF format), so I suspect that the protocol is simply specifying which annotation/assembly version they're talking about.
Your command looks fine, except there is an extra space between "-" and "M" (should b ...
written 7 days ago by
Dave Carlson • 120
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... It's an approximate ML model of amino acid substitution rates that combines useful aspects of previous models (e.g., the applicability to large datasets of the parsimony based methods and the use of likelihood in the ML methods) together into a single model.
You may be interested in reading the pap ...
written 7 days ago by
Dave Carlson • 120
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... To add to this, if you're worried about how long it will take to trim adaptors for a large number of samples, you may want to check out [fastp][1]. It's a very fast, "one-stop-shop" QC program that will trim adaptors, filter and/or trim reads based on quality scores, remove PCR duplicates, and prov ...
written 13 days ago by
Dave Carlson • 120
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... That's a good question. Contamination is not of special concern (this isn't ancient DNA!). I mostly just wanted to be thorough. But yes, all pipelines will involve either mapping to the human reference genome or transcriptome. ...
written 14 days ago by
Dave Carlson • 120
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... Hi Biostars,
I'm currently working on a few pipelines to process and perform various analyses on human RNA-seq data. One of the steps in all of the pipelines is removal of contaminating microbial reads from the input fastq files. Based on recommendations here and elsewhere, I'm using the BBSplit p ...
written 14 days ago by
Dave Carlson • 120
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... Obviously much will depend on your budget and your specific research questions, but as @jared.andrews07 noted, the 1080 is probably not worth the money unless you have specific tasks in mind that utilize graphical processing. I would take the money you plan to put into the GPU and get something wit ...
written 3 months ago by
Dave Carlson • 120
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