Moderator: finswimmer
finswimmer ♦ 10k
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Posts by finswimmer
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... Hello https://www.biostars.org/u/52730/ ,
please use the `ADD REPLY`button below the post you like to reply to.
> I have Written my code but i don’t get the right results.
Then show us the code, the result and your expected result.
> i have a lot of silly questions
Then ask your question! ...
written 4 hours ago by
finswimmer ♦ 10k
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... Hello https://www.biostars.org/u/52753/ ,
have you tried the things mentioned in https://www.biostars.org/p/60263/ ?
Or here: https://gatkforums.broadinstitute.org/gatk/discussion/10115/picard-markdup-error-value-was-put-into-pairinfomap-more-than-once
fin swimmer ...
written 4 hours ago by
finswimmer ♦ 10k
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Comment:
C: Genomics (DNA) Pipeline - Example
... Yes, you need to create an index for the reference genome. How you create this index, depends on the aligner you like to use. E.g. for `bwa` it's a simple `bwa index genome.fa` ...
written 11 hours ago by
finswimmer ♦ 10k
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... Hello https://www.biostars.org/u/52220/ ,
what version of `bcftools` are you using?
Are you sure that `bcftools merge` is the right tool for your purpose? This tools merges vcf file from different samples to one multisample vcf . You have the same sample names in the different files. This should ...
written 12 hours ago by
finswimmer ♦ 10k
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... Oops, sorry my fault. I edited my answer a bit. ...
written 13 hours ago by
finswimmer ♦ 10k
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... Hello https://www.biostars.org/u/50221/ ,
please tell us when you cross-post your question. This question is also asked on [stackexchange][1].
Thanks!
fin swimmer
[1]: https://bioinformatics.stackexchange.com/questions/7080/where-to-download-cancer-raw-reads-fastq ...
written 22 hours ago by
finswimmer ♦ 10k
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... Hello https://www.biostars.org/u/3592/ ,
whether a simple `grep` for the gene name works, depends on if the vcf file is annotated with this information. The best way is to find chromosomal position of your gene of interest (for [ARIH1][1] this is 15: 72,474,326-72,602,985 in case you are using GRCh ...
written 22 hours ago by
finswimmer ♦ 10k
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Comment:
C: bedtools intersect error?
... OK, let's do some more awk-voodoo.
The following code will check for if there are white-spaces in the sequence name and if the start and end position contain only numbers. Those lines that are not valid will be written to `bad.bed`. All others go to `good.bed`, will be sorted and duplicates get r ...
written 23 hours ago by
finswimmer ♦ 10k
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Comment:
C: bedtools intersect error?
... [This explanation][1] makes it more clear what's going on here.
Your `bed` files are malformed. There are lines where the second or third column doesn't contain valid coordinates. This will give you the lines where the second or third column doesn't consist of one ore more numbers:
$ awk -v FS ...
written 1 day ago by
finswimmer ♦ 10k
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Comment:
C: bedtools intersect error?
... According to this [post][1], this error appears if you have duplicate entries in one of your file. Sort your files again after you have remove the white-spaces, but this time use `-u` to remove duplicates:
$ sort -u -k1,1 -k2,2n input > output
[1]: http://seqanswers.com/forums/showthread ...
written 1 day ago by
finswimmer ♦ 10k
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