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Recent Replies
Comment: preforming armitage test on chunks of data in R of VCF file
by
Eliza
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@rpolicastro during wrapup: 0 (non-NA) cases
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Comment: Tools for generating realistic rna-seq reads from reference transcriptome
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GenoMax
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Any read simulation tool should work. `ART `(https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm ) `randomrea…
Answer: RefSeq Transcript vs Reference Genome sequence
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The transcript is the RNA sequence, while the genome sequence is the genomic DNA sequence.
Answer: RefSeq Transcript vs Reference Genome sequence
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RefSeq transcripts are expressed part of the genome. Refseq genome is the entire genome sequence.
Answer: SRA-tools retrieved data of different size compared to ncbi website
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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
by
mhasa006
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70
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
▴
70
Thanks for the reply, will try that.
Comment: Calculating fragment start and end in python
by
iraun
4.8k
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
by
jv
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550
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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mhasa006
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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…
Comment: Calculating fragment start and end in python
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jv
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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
10.0k
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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0
@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
10.0k
Are you doing this on a VCF or the data format in the screenshot?
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