User: finswimmer
finswimmer • 420
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Posts by finswimmer
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... For python2:
file1 = "VMLLVHYAIIGPGLQAKATREAQKRTAAGIMKNPTVDGITVIDLEPISYDPKFEKQLGQVMLLVLCAGQLLLMRTTWAFCEVLTLATGPILTLWEGNPFWNTTIAVSTANIFRGSYLAGAGLAFSLIKNAQTPRRGTGTTGETLGEKRQLNSLDRKEFEEYKRSGILEVDRTEAKSALKDGSKIKHAVSRGSSRWIVERGMVKPKGKVVDLGCGRGGWSYYMATLKNVTEVKGYTKGGP"
file2 = "FWNTTIAVSTANIFRGSYL ...
written 4 hours ago by
finswimmer • 420
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... Hello,
you can tak pythons [str.index()][1] to find the position of a given substring. When you now the starting position, you can calculate the end position by taken the [length][2] of your sequence into account.
fin swimmer
[1]: https://docs.python.org/2/library/stdtypes.html#str.index
[2]: ...
written 8 hours ago by
finswimmer • 420
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Comment:
C: How to do sequencing validation?
... Hello WouterDeCoster,
well checking ngs results is a possible solution in theory. But who is doing that? If I just have a few target genes - ok. But how can I do it economically justifiable for 50, 100 or more genes?
fin swimmer ...
written 8 hours ago by
finswimmer • 420
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... Hello,
when I read about validation in sequencing, there it is always claimed to "establish performance characteristics such as
accuracy, precision, sensitivity, specificity".
But it is absolutly unclear to me, how I can determine this value. Of course I know things that have influence on it. But ...
written 1 day ago by
finswimmer • 420
0
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1
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287
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Comment:
C: gatk tool installation problem
... Which linux distribution do you have? ...
written 6 days ago by
finswimmer • 420
0
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... Hello,
have you read the [manual][1] and know what you are doing, or have you just did copy&paste from somewhere?
What you command is doing is:
1. Remove adapter sequences (ILLUMINACLIP)
2. Remove all bases with a basequality lower than 3 beginning from the
5' end (LEADING)
3. Remove a ...
written 7 days ago by
finswimmer • 420
1
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1
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... Hello,
this doesn't look like a vcf file. It seems to be an input file for ANNOVAR. I don't know for what it is useful, but due to the [manual][1], it seems that "0" means that there is no information about how the Alt looks like.
fin swimmer
[1]: http://annovar.openbioinformatics.org/en/lates ...
written 7 days ago by
finswimmer • 420
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... Hello,
my favorite is [picard HSMetrics][1]. There is also a detailed description of the [metrics][2].
fin swimmer
[1]: https://broadinstitute.github.io/picard/command-line-overview.html
[2]: http://broadinstitute.github.io/picard/picard-metric-definitions.html#HsMetrics ...
written 8 days ago by
finswimmer • 420
1
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1
answer
192
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1
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Comment:
C: No ensemble ID for gene ID
... Hello,
I guess you first have to update your list of gene symbols. In your example 'MLL2' isn't anylonger the official symbol. It's 'KMT2D'. You can see it on [Ensembl][1] or [Genenames.org][2].
fin swimmer
[1]: http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000167548;r=12:49 ...
written 14 days ago by
finswimmer • 420
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111
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Comment:
C: VCF Parser for php
... Hello,
my application will be mainly about displaying informations in the INFO column. So this could be quite easily done, by splitting the columns and the key-value pairs. Things like random access or searching like with a database are not really needed (now).
As I said before, I thought there mi ...
written 15 days ago by
finswimmer • 420
Latest awards to finswimmer
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For A: How to merge multiple bam files into single bam file
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created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
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