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updated 10 hours ago by
Pierre Lindenbaum
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Recent Replies
Comment: How to count the number and proportion of different barcode combinations in DNA
by
dsull
★
6.9k
I have no idea what you’re asking. “185 base sequences”? — i have no idea what that means; do you mean there are 185 possible barcodes? Whe…
Comment: How to count the number and proportion of different barcode combinations in DNA
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GenoMax
146k
Show us a few examples of reads. Since you said `barcode` I assume these are `in-line` in the sequencing read. What is the length of these …
Comment: Clinvar Filter
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GenoMax
146k
Get a BED file of the promoter genomes and then use `bedtools intersect` (https://bedtools.readthedocs.io/en/latest/content/tools/intersect…
Comment: Challenges with Parallelizing BUSCO for Phylogenetic Tree Construction on Large
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GenoMax
146k
A better option is to submit separate SLURM jobs for each genome. Using a `for` loop inside a single SLURM job is not efficient. Instead do…
Comment: How do N's in DNA sequences affect multi-sequence alignments for PCR assay testi
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Ryan
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Thanks! I will check with him and see if this works for him.
Comment: Filtering the vcf file
by
trezini
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I understand how max-depth works, but I asked about max-idepth, indelgap and snpgap
Comment: Parallel AUGUSTUS Execution via GNU Parallel
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GenoMax
146k
Start here: https://www.nextflow.io/
<!-- this is nothing -->
Comment: Parallel AUGUSTUS Execution via GNU Parallel
by
Vijith
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Thank you so much, Dr. Lindenbaum, for the valuable comment. I'm not quite experienced in nextflow, but I like to test this out. Can you pr…
Comment: samtools BGZF block error
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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
9.8k
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
•
0
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
by
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
by
Pierre Lindenbaum
164k
Nice, but you'd better learn to use a workflow manager like snakemake or nextflow. See NF below (not tested):
```
workflow {
c…
Comment: Understanding IGV
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zizigolu
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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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Jaber
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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,
I jus…
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