User: ThePresident

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ThePresident90
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Posts by ThePresident

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Comment: C: Copy number variation using HTSeq/DESeq2
... I totally agree with all of you. I was simply curious but Kevin brought a good argument about different expected distributions in DE vs CNV. Thank you all. ...
written 12 weeks ago by ThePresident90
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Comment: C: Copy number variation using HTSeq/DESeq2
... I will, thank you for the advice. ...
written 12 weeks ago by ThePresident90
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Copy number variation using HTSeq/DESeq2
... I was wondering if the combination of HTSeq / DESeq2 (normally used for differential expression analysis in RNA-seq) could be used for copy number variation in case of DNA sequencing? I can't see why not, but again I didn't look at the math behind DESeq package. Thanks, TP ...
htseq copy number deseq written 12 weeks ago by ThePresident90 • updated 12 weeks ago by WouterDeCoster26k
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Comment: C: DAVID not accepting locus_tag identifiers. Alternatives?
... Thank you Kevin, I really appreciate the effort. One thing I didn't mention is that I have or rather know all bacterial species associated with the locus_tag's. The problem is that some of them contain more relevant info (such as GeneID or "old locus_tag" that is sometimes recognized by DAVID), but ...
written 4 months ago by ThePresident90
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Comment: C: DAVID not accepting locus_tag identifiers. Alternatives?
... Certainly! Here are some representative examples: CTLon_0753 BDI_0296 Msed_0129 YPK_0220 Phep_0329 ECW_m4665 Clo1313_2963 Odosp_2496 Desru_3754 M036_01770 AW19_3420 Thank you for taking a look at this. ...
written 4 months ago by ThePresident90
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DAVID not accepting locus_tag identifiers. Alternatives?
... Related to [my previous post][1], I have a list of genes that have been pooled out from around 60 different bacterial species based on some criteria. Now, I would like to see if there is any functional enrichment in this group. My idea was to use [DAVID][2], however none of the locus_tag inputs are ...
david locus_tag written 4 months ago by ThePresident90
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Comment: C: How to perform functional gene clustering?
... Thank you for clarification. I'll give DAVID a try and see what I get because, as you mentioned, it is an enrichment after all. What I like about DAVID is that it takes locus_tags and thus can deal with anything that has been annotated on NCBI. Also, there seems to be a nice [R package for DAVID][1] ...
written 4 months ago by ThePresident90
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Comment: C: How to perform functional gene clustering?
... Thanks for the suggestions, but I'm afraid these won't do (at least based on the description they give you and the fact that I have list of locus_tags from >200 different species). ...
written 4 months ago by ThePresident90
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How to perform functional gene clustering?
... Let's say I have a gene "A" and I want to know what is a genomic context around it in different bacterial genomes. So, I have looked around "A" in bacterial genome X, Y, Z etc. and I have pulled out a few genes that are in vicinity (both upstream and downstream) of "A" for each one of these X-Y-Z ge ...
david clustering written 4 months ago by ThePresident90 • updated 4 months ago by Kevin Blighe13k
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Comment: C: How to extract only 5-prime hard/soft clipped reads?
... I am not sure I follow. Following your initial suggestions, I should filter for reads: 1. That are soft clipped at the start of the read **but** are mapped on reverse strand (so flagged as 83 or 147 which translates as mapped on reverse strand and being either first or second in pair respectively) ...
written 6 months ago by ThePresident90

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Popular Question 12 weeks ago, created a question with more than 1,000 views. For Extract soft-clipped reads from BWA -generated SAM file

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