Moderator: finswimmer
finswimmer ♦ 6.2k
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Posts by finswimmer
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... With [conda][1] you can easily install any version you like.
[1]: https://www.biostars.org/p/335903/ ...
written 21 hours ago by
finswimmer ♦ 6.2k
1
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... Hello,
Why? [You] [1] [were][2] [told][3] to update to the newest version.
fin swimmer
[1]: https://www.biostars.org/p/343591/#343612
[2]: https://www.biostars.org/p/343591/#343770
[3]: https://www.biostars.org/p/343591/#343833 ...
written 23 hours ago by
finswimmer ♦ 6.2k
0
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73
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Comment:
C: unable to load quant.sf files
... Hello https://www.biostars.org/u/49459/ ,
Please use the formatting bar (especially the `code` option) to present your post better. I've done it for you this time.
Thank you! ...
written 1 day ago by
finswimmer ♦ 6.2k
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... **Why one must masked the PAR region for alignment?**
Let's do some biology to understand this. During meiosis there is a process call crossing over. During this parts of homologues chromosomes are exchange between each other. But what about the case of X and Y chromosome as they don't build a reg ...
written 1 day ago by
finswimmer ♦ 6.2k
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64
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... Hello https://www.biostars.org/u/28277/ ,
- Why do you want to do this?
- The `ignore_truncation` isn't do what you are thinking. From the [manual][1]: `Issue a warning, instead of raising an error if the current file appears to be truncated due to a missing EOF marker. Only applies to bgzipped for ...
written 1 day ago by
finswimmer ♦ 6.2k
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113
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... Hello https://www.biostars.org/u/42413/ ,
again: Update the version!
I edited my commands as I missed the `view` in the `bcftools`command. And as https://www.biostars.org/u/4407/ says the output of `mpileup` must be in a `bcf`format.
fin swimmer ...
written 1 day ago by
finswimmer ♦ 6.2k
1
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0
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113
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0
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... Yes, you're right. Fixed it. ...
written 1 day ago by
finswimmer ♦ 6.2k
1
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1
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140
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1
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... That's a better description about the problem you are trying to solve.
Some ideas:
- Use `tabix` to index your `bed` file. Doing this you can have random access to given regions.
- Think about splitting your regions you want to intersect with and use `gnu parallel`
fin swimmer ...
written 1 day ago by
finswimmer ♦ 6.2k
0
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1
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140
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1
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... It depens on what you want to "intersect". ...
written 1 day ago by
finswimmer ♦ 6.2k
0
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0
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113
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... I think your problem is understanding what is mpileup for. I will try to explain it:
Using samtools/bcftools for variant discovering is a 2-step process.
In the first step - called mpileup - samtools will generate information about each single position of the reference sequence. This contains how ...
written 1 day ago by
finswimmer ♦ 6.2k
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