User: bioinfo89
bioinfo89 • 20
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Posts by bioinfo89
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C: Retrieve genbank viral genomes
... Hi erwan.scoan,
check out this research article ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3324519/ ).
It has a complied list of 32102 viral genomes from GenBank, you can use it directly. Hope that helps!!
...
written 7 weeks ago by
bioinfo89 • 20
• updated
6 weeks ago by
Vijay Lakhujani ♦ 3.0k
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... Thanks EagleEye for the articles I will check them. ...
written 7 weeks ago by
bioinfo89 • 20
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... Hi All,
I have a list of variants and I want to integrate the data from GTex database. Is there any specific way to do this?
The files provided on the GTEx portal are quite complicated to understand.
I want to extract the information related to variant and its expression in all the tissues. (eg. i ...
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... Hi Nandini,
Could you suggest what parameter to take using select variants which would help to achieve what I want?
Thanks! ...
written 3 months ago by
bioinfo89 • 20
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... I have one vcf per sample! Thanks I will try this! ...
written 3 months ago by
bioinfo89 • 20
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... Hi All,
I have been working on targeted amplicon sequencing data (>200 samples). I use GATK for variant calling. So my question is, is there a parameter in variant calling where we can specify to not call variants if the reference allele frequency is say >0.8 than the alternate allele frequen ...
written 3 months ago by
bioinfo89 • 20
• updated
3 months ago by
finswimmer ♦ 5.4k
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... I used it to get the result. But the mapped regions were scattered. (eg. 1 to 63 of the query mapped to different coordinate, 64 to 123 mapped to different coordinate etc). ...
written 3 months ago by
bioinfo89 • 20
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... Blastn from Ensembl! ...
written 3 months ago by
bioinfo89 • 20
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... No it gives the corresponding nucleotide sequence (known Genbank accession ID). ...
written 3 months ago by
bioinfo89 • 20
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... Hi all,
I am working on breast cancer data. I have protein sequence for BRCT domain and I want know its nucleotide sequence coordinates. I tried using tblastn to get the corresponding nucleotide sequence (~294bp) and then I used ensemble blast to get the coordinates of the nucleotide sequence obtai ...
written 3 months ago by
bioinfo89 • 20
Latest awards to bioinfo89
Scholar
4 months ago,
created an answer that has been accepted.
For A: How to extract unique paired end reads from a merged BAM file?
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