User: H.Hasani

gravatar for H.Hasani
H.Hasani580
Reputation:
580
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Trusted
Location:
Freiburg, Germany
Last seen:
8 hours ago
Joined:
1 year, 11 months ago
Email:
h*************@yahoo.com

Posts by H.Hasani

<prev • 131 results • page 1 of 14 • next >
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Comment: C: Recognizing an organism which is combination of other organisms
... Sounds to me like a problem for phylogenetics .. don't know how much it will help you, but have tried clustering by conservation information? ...
written 3 months ago by H.Hasani580
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Comment: C: samtools view region
... Oh, I see your point now. ...
written 4 months ago by H.Hasani580
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Answer: A: functional variant discovery after GATK variant calling
... I'm all for [VEP][1] [1]:http://www.ensembl.org/info/docs/tools/vep/index.html ...
written 4 months ago by H.Hasani580
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Comment: C: samtools view region
... could you point out where did you read that? when it comes to intersection it does not matter which end is obtained by the given list of intervals (at least that's what they say specifically in case of paired-end reads). ...
written 4 months ago by H.Hasani580
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Comment: C: samtools view region
... > -abam Default behavior when using BAM input (deprecated since 2.18.0) it says deprecated (the -abam), but you still can use -a and -b as given in this example ...
written 4 months ago by H.Hasani580
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Comment: C: TCGA raw counts DexSeq
... no problem, no one was born knowing it all ;) just go to their page and check how each tool works and what is the accepted format (they have plenty of examples), e.g. intersect takes files format BAM/BED/GFF/VCF so you need to make sure both files (your counts & gtf) follows one of those format ...
written 4 months ago by H.Hasani580
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Answer: A: Broad rules of thumb on # of variations
... I think it is quite problematic to think of SNPs as a number; annotating the variants or compute basic overlap with the annotation is the scientific methodology to do it. Numbers can rely on many factors as everybody pointed out. I'm afraid, this way of thinking will consume your time instead of spe ...
written 4 months ago by H.Hasani580
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Answer: A: TCGA raw counts DexSeq
... IMHO, you can annotate your RNA-Seq file. For example, you extract transcripts entries from your gtf, then using bedtools (intersect, overlap, or closest) to map both files. Withj some basic bashing you can then transform the results into the format you need. hth ...
written 4 months ago by H.Hasani580
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Answer: A: samtools view region
... How about running [bedtools - intersect][1] on your bam file. That should you give you what you want. I just noticed, there is already an example of exactly what you are after on that page. [1]: http://bedtools.readthedocs.io/en/latest/content/tools/intersect.html ...
written 4 months ago by H.Hasani580
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Comment: C: GEO datasets: Raw data is available on Series record
... Not really, I was referring to his (b) question, if raw data was mentioned to be available, yet you can't find it...what to do > Raw data is available on Series record and this is where i am facing a problem. I cannot access these files. ...
written 4 months ago by H.Hasani580

Latest awards to H.Hasani

Scholar 3 months ago, created an answer that has been accepted. For A: csv into genome browser
Scholar 4 months ago, created an answer that has been accepted. For A: csv into genome browser
Commentator 7 months ago, created a comment with at least 3 up-votes. For A: How many SNPs are sufficiant for covering?
Centurion 12 months ago, created 100 posts.
Voter 16 months ago, voted more than 100 times.
Commentator 16 months ago, created a comment with at least 3 up-votes. For A: How many SNPs are sufficiant for covering?
Commentator 17 months ago, created a comment with at least 3 up-votes. For A: How many SNPs are sufficiant for covering?
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Commentator 23 months ago, created a comment with at least 3 up-votes. For A: How many SNPs are sufficiant for covering?
Scholar 23 months ago, created an answer that has been accepted. For A: How many SNPs are sufficiant for covering?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: How many SNPs are sufficiant for covering?

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