Moderator: finswimmer

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finswimmer2.7k
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Posts by finswimmer

<prev • 473 results • page 1 of 48 • next >
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Answer: A: conversion of GFF3 formate to BED format
... Hello, you could use `ggf2bed` from [BEDOPS][1] $ gff2bed < foo.gff3 > foo.bed fin swimmer [1]: http://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gff2bed.html ...
written 5 hours ago by finswimmer2.7k
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Comment: C: Tool to do Variant calling from contigs data
... Hello, I don't know whether the restriction mentioned in this [post][1] still exists. So be careful. fin swimmer [1]: https://www.biostars.org/p/135900/#135902 ...
written 6 hours ago by finswimmer2.7k
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Comment: C: Tool to do Variant calling from contigs data
... Hi de.mecquenem.ninon, This reply is better suited as a comment on Carambakaracho's answer. Answers should ONLY be used to respond to the original question at the top of this page. I moved your post to a comment. But as you see this is not perfect. fin swimmer ...
written 6 hours ago by finswimmer2.7k
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Comment: C: Check if BAM is derived from pair-end or single-end reads?
... Hello Hakubi and welcome to biostars, your post is better placed as a comment. To do this please use the `ADD COMMENT` button below the post you like to reply to. Answers should only be used to respond to the original question at the top of this page and should answer the question as best as possib ...
written 8 hours ago by finswimmer2.7k
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Comment: C: sortsam (picard) error in identifyting samfile
... > It is because I used, nohup? Yes, you are right. From `nohup --help`: If standard error is a terminal, it is redirected to standard output. I think you can repair your sam file by removing all lines that starts with `[` grep -v "^[" SRR6876052_mem.sam > repaired.sam ...
written 9 hours ago by finswimmer2.7k
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Comment: C: sortsam (picard) error in identifyting samfile
... You're correct, These status message shouldn't be in the sam file. In the command you gave above I cannot see why this happens. Standard questions at this point: What version of bwa are you using? Which OS are you using? fin swimmer ...
written 9 hours ago by finswimmer2.7k
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Comment: C: sortsam (picard) error in identifyting samfile
... To get the whole header: grep "@" SRR6876052_mem.sam To get the first 10 lines that are not the header: grep -m 10 -v "^@" SRR6876052_mem.sam ...
written 10 hours ago by finswimmer2.7k
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Comment: C: sortsam (picard) error in identifyting samfile
... Hello again, those lines starting with `@` are the header lines. Beside this we need the first few lines that doesn't start by `@.` fin swimmer BTW: It's better to use the `code` formating button for file contents as well. ...
written 10 hours ago by finswimmer2.7k
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Comment: C: sortsam (picard) error in identifyting samfile
... Hello shuksi, could you please post the first lines of your sam file? How have you produced this file? fin swimmer ...
written 10 hours ago by finswimmer2.7k
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Answer: A: Get every variables sites between two aligned CDS sequences
... Here the new script based on the [new criterias][1]: https://gist.github.com/finswimmer/7b540d695fede0fdb10120d53afab2ca Output now looks like this: #POS species3 species1 effect_s1 species2 effect_s2 7 C A non-synonymous T non-synonymous 15 G ...
written 1 day ago by finswimmer2.7k

Latest awards to finswimmer

Scholar 1 day ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 2 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 8 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 11 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 12 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 12 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 27 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 28 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 28 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 29 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 4 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 6 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Voter 7 weeks ago, voted more than 100 times.
Scholar 7 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 7 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 8 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file

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