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when I use htslib to write a bam. Error of "truncated file" shows by samtools
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
vg call - Selecting reference path to call on
Answer: vg call - Selecting reference path to call on
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Answer: when I use htslib to write a bam. Error of "truncated file" shows by samtools
by
John Marshall
3.0k
There are several problems with this code: 1. You have not set `b->l_data`, which here should be set to the same value as `b->m_data`. T…
Comment: Best practices in Fungal Genome Assembly
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Umer
▴ 50
Should I use both Recon and Pilon for polshing ? Recon uses Long-reads and Pilon uses short-read. if both should be used, is their any pref…
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garcesj
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How come? If I have a pro-tumorigenic product, for example, wouldn't this comparison be valid?
Comment: How to Convert CNV Data to CNA Format for Reproducing Results with the Padma Pac
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Ngrin
• 0
Thanks @Zhenyu Zhang for your response. I have just looked at the files you mentioned. Do you have any recommended package or code snippet …
Comment: coding and non-coding region of the viral genome
by
Ghada
• 0
As far I understand non coding region equal to the intergenic region? please can you write an example for how to calculate one region ? I…
Comment: when I use htslib to write a bam. Error of "truncated file" shows by samtools
by
Pierre Lindenbaum
162k
Thanks for the code, it's interesting. It doesn't solve the problem , but the code is missing `#include <htslib/bgzf.h>` and I cannot fin…
Comment: How to Convert CNV Data to CNA Format for Reproducing Results with the Padma Pac
by
Zhenyu Zhang
★ 1.2k
In the GDC, there are raw float value CNV data, and integer CNV values after advanced modeling. If you only want those floating-point numbe…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
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Ram
44k
Please edit your original post and add this at the top so everyone reads that first. GeneCards politely asks people not to scrape - not res…
Comment: I cannot download VG in any way
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Ram
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In that case, OP should have said "Cannot install SequenceTube", since that is the problem, not vg. Maybe this is the SequenceTube that OP…
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GenoMax
142k
I read that to mean that the only way they were able to download `vg` was by using `conda`. Since `SequenceTube` (whatever that is) require…
Comment: I cannot download VG in any way
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Ram
44k
> The only way that I managed to download vg is using conda, however since my primary goal is to download SequenceTube You're mentioning t…
Comment: I cannot download VG in any way
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Ram
44k
Also, OP buries the lede and uses a misleading title. They are able to install vg using conda, but that is secondary to them using a differ…
Comment: Can I count UMI-barcode combination without mapping?
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GenoMax
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You can use some code I have here for inspiration: https://www.biostars.org/p/270737/#270753 You can extract the UMI by using. $ awk…
Comment: Best practices in Fungal Genome Assembly
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samuel.a.odonnell
▴ 540
I think 10 rounds in excessive. I usually only run 1-3 rounds (as long-read accuracy has improved I have used fewer and fewer rounds), but …
Comment: I cannot download VG in any way
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GenoMax
142k
Why are you not downloading the `vg` binaries provided here: https://github.com/vgteam/vg/releases/tag/v1.57.0 Use the `Click here to Downl…
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