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Recent Replies
Comment: preforming armitage test on chunks of data in R of VCF file
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Eliza
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@rpolicastro during wrapup: 0 (non-NA) cases
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
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Any read simulation tool should work. `ART `(https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm ) `randomrea…
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The transcript is the RNA sequence, while the genome sequence is the genomic DNA sequence.
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RefSeq transcripts are expressed part of the genome. Refseq genome is the entire genome sequence.
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Never use file sizes as a metric for anything other than for qualitative purpose (e.g. a file is non-zero bytes so must have something).
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Comment: Calculating fragment start and end in python
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mhasa006
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Well, that is true, but it is part of a bigger project. And calling third-party tools can be problematic. Either way, thanks for the reply.
Comment: Calculating fragment start and end in python
by
mhasa006
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Thanks for the reply, will try that.
Comment: Calculating fragment start and end in python
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iraun
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Do you need to to this in python? There are tools already out there performing these kind of tasks, such as [CollectInsertSizeMetrics (pica…
Comment: Calculating fragment start and end in python
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jv
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how about filtering the BAM file for the region on interest and then converting the output to a BED file which will contain the read start …
Comment: Calculating fragment start and end in python
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Actually, I'm fetching reads form a BAM file that is within a bed region. Then I'm trying to calculate the fragment start/end of the fetche…
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would `bedtools bamtobed` get you what you want? <https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html>
Comment: preforming armitage test on chunks of data in R of VCF file
by
rpolicastro
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This can also be done with list columns but I think splitting the data is a little syntactically clearer.
```
library("dplyr")
library("CAT…
Comment: preforming armitage test on chunks of data in R of VCF file
by
Eliza
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0
@rpolicastro on data frame format
Comment: genotype encoding
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Eliza
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@David Carlson . doea it mean that if i have a file that contains ony SNPs the encoding cant be zero?"A site with a homozygous reference ge…
Comment: preforming armitage test on chunks of data in R of VCF file
by
rpolicastro
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Are you doing this on a VCF or the data format in the screenshot?
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