User: Angel

gravatar for Angel
Angel10
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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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a************@protonmail.com

Posts by Angel

<prev • 10 results • page 1 of 1 • next >
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Comment: C: False positives in manta structural variant calling
... I see, I will try my best to filter out all irrelevant info. Thanks a lot for your input! ...
written 3 months ago by Angel10
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Comment: C: False positives in manta structural variant calling
... 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 Angel10
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False positives in manta structural variant calling
... 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 "^#" | ...
sv structural variants wes manta written 3 months ago by Angel10
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Comment: C: Visual summary from a collection of .vcf files (WES)
... That´s exactly my use case, thank you! ...
written 6 months ago by Angel10
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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 Angel10
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Comment: C: Visual summary from a collection of .vcf files (WES)
... 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 Angel10
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Visual summary from a collection of .vcf files (WES)
... 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 ...
vcf wes summary visual variants written 6 months ago by Angel10
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Comment: C: rsem-parse-alignments failed due to bowtie-produced partial alignments
... Bowtie2 analysis worked. ...
written 22 months ago by Angel10
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Comment: C: rsem-parse-alignments failed due to bowtie-produced partial alignments
... 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 Angel10
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rsem-parse-alignments failed due to bowtie-produced partial alignments
... 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 ...
rsem bowtie written 22 months ago by Angel10 • updated 22 months ago by swbarnes29.6k

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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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