User: jared.andrews07

gravatar for jared.andrews07
Reputation:
730
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Trusted
Location:
Washington University in St. Louis
Website:
https://github.com/j-a...
Last seen:
1 day, 18 hours ago
Joined:
11 months, 4 weeks ago
Email:
j**************@gmail.com

Ph.D. candidate at Washington University in St. Louis. I have a strong interest in the development of high-performance, flexible bioinformatic tools that can integrate multiple -omics datasets to yield interesting and plausible conclusions that can then be experimentally validated.

Avid Python user and fledgling developer. Strange fascination with ostriches.

Posts by jared.andrews07

<prev • 116 results • page 1 of 12 • next >
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Answer: A: have trouble to upload data to washU browser
... You need to put `track type=bedGraph` as the first line in your file, at a minimum. See the [bedgraph format guidelines](https://genome.ucsc.edu/goldenpath/help/bedgraph.html) for other options, as stated in genomax's comment.. ...
written 3 days ago by jared.andrews07730
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Comment: C: Using RIPSeeker : RIPSeeker terminates with the "cannot allocate memory" error
... The error is pretty straightforward - you don't have the memory to run it with all processing cores available. Either run it on a cluster with the appropriate resources or don't use the multicore option - those are pretty much your only choices. ...
written 3 days ago by jared.andrews07730
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Comment: C: the bam file used for Diffbind
... Typically I leave them in, as many programs ignore them. ...
written 5 days ago by jared.andrews07730
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Answer: A: the bam file used for Diffbind
... Yes, it is a good idea to remove blacklisted reads before using DiffBind. I usually don't bother removing duplicates unless I have an unusually high percentage of them - particularly for factors with sharp peaks where some duplication is expected. The FRiP really depends on your sample and how hea ...
written 5 days ago by jared.andrews07730
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Answer: A: weird problem with summit.bed file from macs2
... The summits file is just that - the summit of each peak. It's showing the position (base) for each peak that has the highest signal. That's what they're supposed to look like. ...
written 5 days ago by jared.andrews07730
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Comment: C: finding mutations in rna-seq transcriptome
... It seems the `two-pass` mode isn't available on Galaxy, but STAR isn't too hard to set up locally if you've got enough RAM. It's kind of a hog, so you want at least 32 GB for it to run. ...
written 16 days ago by jared.andrews07730
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Comment: C: DESEQ2 results - write to TSV file
... He's saying it's an easy solution - he just didn't know where to look. ...
written 17 days ago by jared.andrews07730
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Answer: A: finding mutations in rna-seq transcriptome
... You can use same tools used for finding them in whole genome sequencing. Be aware that most of your reads are only coming from one strand the majority of the time with RNA-seq, so het/homozygous calls are a lot less reliable. [GATK](https://software.broadinstitute.org/gatk/) is kind of the standard ...
written 17 days ago by jared.andrews07730
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Comment: C: Motif database of choice
... CIS-BP hasn't been updated since 2015, so it has a lot of 'inferred' motifs for TFs that HOCOMOCO has direct evidence for instead, as it's continually updated. I would use HOCOMOCO or JASPAR over CIS-BP personally, though calling them 'better' is somewhat subjective. ...
written 28 days ago by jared.andrews07730
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Comment: C: Differential expression between two biological samples sequenced with single-cel
... Is there any reason DESeq or EdgeR wouldn't work for this? ...
written 11 weeks ago by jared.andrews07730

Latest awards to jared.andrews07

Teacher 11 days ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Supporter 16 days ago, voted at least 25 times.
Centurion 3 months ago, created 100 posts.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 6 months ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Scholar 8 months ago, created an answer that has been accepted. For A: How to make variant calling run faster?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
Autobiographer 11 months ago, has more than 80 characters in the information field of the user's profile.

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