User: prasundutta87

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prasundutta87190
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Posts by prasundutta87

<prev • 117 results • page 1 of 12 • next >
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Comment: C: autosomal ancestry inference
... Since you are already using admixture software, check out its manual: http://www.genetics.ucla.edu/software/admixture/admixture-manual.pdf I am not sure why the link is not opening, probably some updation is going in the server where it is stored, but, in the document, an explanation has been provi ...
written 2 days ago by prasundutta87190
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Comment: C: PCA implementation in plink
... Thanks a lot Christopher!! ...
written 12 days ago by prasundutta87190
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PCA implementation in plink
... Hi, Can someone point out to a document or explain how plink is calculating Principal components? I am not asking how to do it. I have already done it. I just wanted to know how is it considering the genotype values from a VCF file to calculate the principal components. ...
population pca plink written 13 days ago by prasundutta87190 • updated 12 days ago by chrchang5233.7k
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Comment: C: query on a pre-process step involving GFF3
... Thanks, Sej..I have the other way round issue..I updated my GFF3 file chromosome names to match my reference genome.. ...
written 14 days ago by prasundutta87190
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query on a pre-process step involving GFF3
... Hello, So, I had to update the chromosome names in a GFF3 file. For ease, I removed the lines that started with #. This helped me to get a clean tab separated GFF3 file that I could use in my R script for updating the chromosome names. The reason I removed the lines because some lines had something ...
gff3 annotation written 14 days ago by prasundutta87190
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Comment: C: some questions on GFF3
... Thanks a lot h.mon.. ...
written 15 days ago by prasundutta87190
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some questions on GFF3
... Hi, Can someone explain me in a little more detail these gff3 annotations? NW_020229148.1 Gnomon exon 23509 23858 . - . ID=id836183;Parent=id836181;Dbxref=GeneID:112582887;gbkey=V_segment;gene=LOC112582887;model_evidence=Supporting evidence includes similarity to: 83%25 coverage of the annotat ...
gtf annotation gff written 15 days ago by prasundutta87190
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Answer: A: gffread query for gff to gtf conversion
... Got this reply.. GTF is a transcript-oriented format, it only supports a very limited set of features (as opposed to GFF3), namely only transcript-describing features (exon, CDS and that's pretty much it). The "region" feature here is not something that GTF cares about -- and frankly neither does g ...
written 17 days ago by prasundutta87190
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Comment: C: gffread query for gff to gtf conversion
... I have posted this question in the gffread github page just now. Hopefully, I may get a reply there..if I get it soon, I will post the reply here as well.. ...
written 19 days ago by prasundutta87190
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gffread query for gff to gtf conversion
... Hi, I was just wondering if one can explain to me what is happening with the tool gffread while converting one gff file to gtf file. I used the following command: gffread -T -o When I checked the unique chromosomes/scaffold names to check if the conversion was correct, both gff file and gtf ...
gtf annotation gff software written 20 days ago by prasundutta87190

Latest awards to prasundutta87

Popular Question 13 days ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Centurion 6 weeks ago, created 100 posts.
Supporter 3 months ago, voted at least 25 times.
Scholar 12 months ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: SNPEFF for de novo transcriptome annotation

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