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Recent Replies
Comment: samtools BGZF block error
by
Pierre Lindenbaum
164k
> I cannot use it in anyway?
you shouldn't. Run `samtools view -c in.bam ` on this file, and you should get the same error if I'm not wr…
Comment: Filtering the vcf file
by
Medhat
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I hope this may help:
https://www.biostars.org/p/99940/#99958
For the depth part, let us assume we used the following command `bcftools …
Comment: samtools BGZF block error
by
Novice
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Pierre, thank you. When you say broken/corrupted does it mean I cannot use it in anyway? i was able to run samtools mpileup just this week …
Answer: samtools BGZF block error
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Pierre Lindenbaum
164k
your file input.bam is broken/corrupted. There is nothing you can do but regenerating this file.
Answer: Parallel AUGUSTUS Execution via GNU Parallel
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Pierre Lindenbaum
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Nice, but you'd better learn to use a workflow manager like snakemake or nextflow. See NF below (not tested):
```
workflow {
c…
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I am very new to IGV I am not sure how to do that I took several screenshot because I do not know which part is the mutation I want
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Could you please tell me how can I access inflammatory genes for certain organs to study like wanna study inflammatory genes in HCC,
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`RefSeq` is actually curated subset of GenBank. The sequences will be non-redundant and will save you time/effort: https://ncbi.nlm.nih.gov…
Comment: How do N's in DNA sequences affect multi-sequence alignments for PCR assay testi
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I am using clustal omega to perform the alignments. My friend is required to use genbank so I believe I'm stuck with it for this tool
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Depending on the program you are using solitary N's may not have deleterious effect on your testing. You may want to use curated sequences …
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Please do not ask similar question in different threads: https://www.biostars.org/p/9603180/
You can also follow up on individual papers (…
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My main point was that instead of `you can set threshold where you think is reasonable` it should be `you can set threshold where you think…
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