User: Angel
Angel • 10
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- 10
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- New User
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- Last seen:
- 2 months, 2 weeks ago
- Joined:
- 1 year, 10 months ago
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Posts by Angel
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... I see, I will try my best to filter out all irrelevant info. Thanks a lot for your input! ...
written 3 months ago by
Angel • 10
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... Thank you. Even if filtering by "MantaBND" also includes domestic insertions, don't you think the numbers are very high? ...
written 3 months ago by
Angel • 10
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... Hi guys,
I'm analyzing **structural variants** in paired tumor-healthy human samples with **[manta][1]** and I was surprised by the huge number of events identified by the software, particularly in terms of translocations (MantaBND). Just a couple examples:
`gzcat somaticSV.vcf.gz | grep -v "^#" | ...
written 3 months ago by
Angel • 10
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... That´s exactly my use case, thank you! ...
written 6 months ago by
Angel • 10
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Answer:
A: Pathways Analysis - pvalue
... If you are running an **enrichment test**, yes, the longer the list of genes, the higher the probability of finding an overlap by chance and therefore the higher the p-value. ...
written 6 months ago by
Angel • 10
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... I use VEP (there was a typo in my original message), I was just wondering if there is a tool to generate visual summaries in an easy way. ...
written 6 months ago by
Angel • 10
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... Hi guys,
I was wondering whether there is any available software to produce a **visual summary** from a collection of annotated *.vcf files* (say, the output of VEP). Something similar to the left panel in [this figure][1], which includes total number of variants, number of samples in which the gen ...
written 6 months ago by
Angel • 10
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... Bowtie2 analysis worked. ...
written 22 months ago by
Angel • 10
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... Thank you for your answer. I was very surprised that bowtie, the **default** aligner used by RSEM, produced an "incompatible" alignment; indeed this is the first time I encounter this kind of error. It seemed more plausible that the error came from the parameters I passed to bowtie, so I re-ran the ...
written 22 months ago by
Angel • 10
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... Hi guys,
I'm getting a weird error running *rsem-calculate-expression*, I hope you can point me in the right direction.
**RSEM version:** 1.3.0
**Bowtie version:** 1.2.0
**RSEM indexes** (for *bowtie* and *bowtie2*) were generated as follows:
rsem-prepare-reference --gtf /home/aalvarez/scra ...
Latest awards to Angel
Popular Question
12 weeks ago,
created a question with more than 1,000 views.
For rsem-parse-alignments failed due to bowtie-produced partial alignments
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