User: jc.szamosi

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jc.szamosi50
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Canada
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Posts by jc.szamosi

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Using GATK4 Mutect2 on mouse data, need a genome snp reference
... I can skip it, and that's what I've done for now. For technical reasons, my tumor and normal samples need to come from different individuals. I've created a PON from all my normal individuals, but I was hoping for a strain vcf so that I can try to distinguish between among-individual variation in th ...
written 20 months ago by jc.szamosi50
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Comment: C: Using GATK4 Mutect2 on mouse data, need a genome snp reference
... Thanks! Do you know of a way to make the snp file work with GATK4 if the POP_AF tag is absent? ...
written 20 months ago by jc.szamosi50
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Comment: C: Using GATK4 Mutect2 on mouse data, need a genome snp reference
... The link to the NCBI vcfs in that tutorial is broken, but I'll see if I can find one that works and edit this comment. Edit: The NCBI vcf files are here: ftp://ftp.ncbi.nih.gov/snp/organisms/archive/mouse_10090/VCF/, but they also don't have POP_AF INFO tags, so they won't work for this purpose. Ma ...
written 20 months ago by jc.szamosi50
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Using GATK4 Mutect2 on mouse data, need a genome snp reference
... I am using the Mutect2 program from GATK4 to call somatic snps in mouse cancer cells, and I want to use the Sanger Mouse genome project's strain-specific vcf file (ftp://ftp-mouse.sanger.ac.uk/) for the `--germline-resource` argument, but this argument requires that the vcf file have a `POP_AF` INFO ...
vcf gatk mutect2 snp mouse written 20 months ago by jc.szamosi50
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Comment: C: Mouse RNASeq, 50% discordant reads
... I used bamUtil's clipOverlap to create a file of only the overlapping reads, and used samtools flagstat to count them. The percentage of overlapping reads in this sample is not greater than in other samples, so I don't think that's the issue. ...
written 4.2 years ago by jc.szamosi50
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Comment: C: Mouse RNASeq, 50% discordant reads
... It may be. The fragment sizes are ~300bp including adapter (so ~150 without). But the other samples have the same size distribution and don't have this problem. Is there a quick way to check if discordant reads are overlapping or do I need to write a script? ...
written 4.2 years ago by jc.szamosi50
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Mouse RNASeq, 50% discordant reads
... I have an RNASeq sample with mouse data that started with a very low amount of RNA. We did a test run on the MiSeq, trimmed the reads to 75bp, and ran it through TopHat just to see how it's looking. For the most part it seems fine (no bias to 3' end of genes, 75% mapping rate (low but not terrible) ...
rna-seq written 4.2 years ago by jc.szamosi50
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Analyzing RNA Seq splice variants using spike-ins?
... I'm about to start a splice variant analysis in RNASeq, and I was wondering if anyone has done this using spike-in controls. I see that ERCC normalization can't be combined with CuffDiff2, because CuffDiff2 has its own normalization, but I was wondering if anyone is using ERCC controls anyway just ...
rna-seq written 4.3 years ago by jc.szamosi50 • updated 3.7 years ago by Satyajeet Khare1.5k
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Answer: A: Indexing Tables erros during readcufflinks
... Okay, I think I've figured this out. It looks like this is a warning that reshape2's `melt()` function produces when you're trying to melt different factor columns into a single value column. I suspect (haven't dug through the source) `readCufflinks()` is using `melt()` internally when it creates th ...
written 4.4 years ago by jc.szamosi50
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Answer: A: Indexing Tables erros during readcufflinks
... I'm getting the same warning. I wish the message was more informative (which attributes, which variables). I have no idea if this is something I should be worrying about or not. Presumably I'm losing some information, but how much? ...
written 4.4 years ago by jc.szamosi50

Latest awards to jc.szamosi

Popular Question 4.1 years ago, created a question with more than 1,000 views. For Installing And Running Antismash
Popular Question 4.1 years ago, created a question with more than 1,000 views. For htseq-count overcounting non-unique alignments

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