User: finswimmer
finswimmer • 1.4k
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Posts by finswimmer
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... Hello hbleed121,
what kind of trouble are your facing? Please be more specific. Or is it just a general coding question about how you can make your code faster, shorter, more beautiful, .... ?
fin swimmer ...
written 1 day ago by
finswimmer • 1.4k
0
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2
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101
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2
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... Hello bioinfo89,
the idea was using bbduk to remove your primer sequences from your reads and not just the adapters. So if you already removed your adapters trimm your data a second time using bbduk and provide a "adapter file" containing the sequences of your primers.
fin swimmer ...
written 2 days ago by
finswimmer • 1.4k
0
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2
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101
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2
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... Hello bioinfo89,
as genomax said it's a better idea to trim your data using the adapter trimming function from [bbduk][1].
fin swimmer
[1]: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/ ...
written 3 days ago by
finswimmer • 1.4k
0
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3
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76
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3
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... Hello arsala521,
you can filter with [SnpSift][1]. Especially have a look at the part "Available operands and functions".
fin swimmer
[1]: http://snpeff.sourceforge.net/SnpSift.html#filter ...
written 3 days ago by
finswimmer • 1.4k
3
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1
answer
75
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1
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... Hello,
have a look at [snpEff][1]. Your list of SNP/indel have to be in vcf or bed format.
fin swimmer
[1]: http://snpeff.sourceforge.net/SnpEff_manual.html ...
written 3 days ago by
finswimmer • 1.4k
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90
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0
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Comment:
C: Picard Mark Duplicates
... > Regarding the soft clip bases, I don't think soft clipped bases has to
> do with this thing because the position 88015806 in the above example
> is the position start of the alignment and not the soft clipped bases.
You're right. The alignment starts with the first not soft clipped base. ...
written 4 days ago by
finswimmer • 1.4k
0
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90
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0
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Comment:
C: Picard Mark Duplicates
... > The MarkDuplicates tool works by comparing sequences in the 5 prime
> positions of both reads and read-pairs in a SAM/BAM file.
Oh, have they changed their algorhithm or just the explanation? I have in mind, that picard MarkDuplicate doesn't compare any sequence, but look at the most 5' map ...
written 4 days ago by
finswimmer • 1.4k
4
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3
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211
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3
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Answer:
A: SNPs in 1000 genome project
... Hello Javad,
without a little work you will not reach your goal. The most difficult part here is, to clarify who said what is an exon? UCSC, NCBI, Ensembl,...? And do you want just coding exons or all?
Let's assume you like all exons defined by NCBI.
1. Go to [UCSC Table browser][1]
2. Choose hg ...
written 5 days ago by
finswimmer • 1.4k
1
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2
answers
177
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2
answers
... Beside the correct question from Ram why you want to do this, here is a python solution:
from Bio import SeqIO
original_file = "./original.fasta"
extended_file = "./extended.fasta"
with open(original_file) as original, open(extended_file, 'w') as extended:
records ...
written 5 days ago by
finswimmer • 1.4k
1
vote
0
answers
102
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0
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Comment:
C: phasing vcf file
... Hello,
have a look into the [manual][1]. The Stack needs more memory. You can set the size with the `–Xss` parameter. For example use `–Xss5m` to set the stack size to 5Mb.
Please use the code button to mark code. It is better to read.
And if you found a post helpful please upvote it.
fin swimme ...
written 5 days ago by
finswimmer • 1.4k
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For A: How to merge multiple bam files into single bam file
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