User: bitpir

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bitpir60
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Posts by bitpir

<prev • 28 results • page 1 of 3 • next >
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Comment: C: Glimmer output file
... Good catch! Thought of another question but forgot to change the grammar! :) ...
written 10 hours ago by bitpir60
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Glimmer output file
... Hi, I am not quite understanding the output of the .predict file from Glimmer3.02 ORF predictor. Here's a sample of the output file ref|NC_023013.1| Haloarcula hispanica N601 chromosome 1, complete sequence orf00001 1 1575 +1 18.88 orf00003 2355 1645 -1 12.8 ...
orf prediction glimmer3 written 11 hours ago by bitpir60
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Comment: C: how does Agilent/xGen design hybridization probes?
... Excellent, this is what I'm looking for! Thank you so much :) ...
written 10 weeks ago by bitpir60
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how does Agilent/xGen design hybridization probes?
... I'm curious about how Agilent/IDT design exome hybridization probes, how do they ensure that (i)the probes won't self-anneal, (ii) mostly capturing exonic regions, (iii) GC content and (iv) annealing temp of each probe to fragmented DNA are similar? Is there a free software (like PCRTiler) available ...
exome sequencing custom probes written 10 weeks ago by bitpir60 • updated 10 weeks ago by jean.elbers160
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Comment: C: best way to do joint genotyping
... great! Thanks for the tip! ...
written 11 weeks ago by bitpir60
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Comment: C: best way to do joint genotyping
... Hi Ram, I don't need to analyze each of them separately, but was planning to analyze on per family basis as some genes could be dominant/recessive/compound hets, etc. Thanks for the advice! ...
written 11 weeks ago by bitpir60
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best way to do joint genotyping
... I have exome sequences from 6 families (~38 samples) of European descent with similar hereditary diseases (e.g. epilepsy). Each family is supposedly unrelated. Some samples are from healthy family members, others are infected. What's the best way to do joint genotyping for this type of analysis? Sho ...
joint-genotyping gatk vcf written 11 weeks ago by bitpir60 • updated 5 weeks ago by Biostar ♦♦ 20
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Answer: A: how to plot multi pheatmap into one figure
... Hi all, I know my answer is ~3years too late but I just want to put it out there and hopefully people will find this useful in the future. I found the answer [here][1] Basically, user hrbrmstr mentioned that "The manual page for pheatmap() clearly states in the Values section that it returns a list ...
written 4 months ago by bitpir60
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Answer: A: do blast search using gi numbers
... Hi all, Thank you for the responses. Somehow I am able to use GI numbers as queries for rpsblast using ncbi-blast-2.6.0. This was also tested by Dr. Wayne Matten from NCBI User Services.Here's what I did: 1. Sort and output only unique GI numbers, else a C++ exception error will occur (see htt ...
written 8 months ago by bitpir60 • updated 8 months ago by genomax46k
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Answer: A: ncbi error C++ exception
... Thank you for your responses! I think I figured out the error. This happens when there's duplicate queries in the file (1400_to_4999_combined_protein_id_ac, which contains gi numbers). If I sort and output the unique gi numbers, the C++ error went away. The error "Protein BLAST database 'Pfam nr' do ...
written 8 months ago by bitpir60

Latest awards to bitpir

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: how to plot multi pheatmap into one figure
Scholar 8 months ago, created an answer that has been accepted. For A: do blast search using gi numbers
Popular Question 14 months ago, created a question with more than 1,000 views. For samtools counting unique mapped reads

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