User: ThePresident

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ThePresident90
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Posts by ThePresident

<prev • 72 results • page 1 of 8 • next >
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Comment: C: Extracting multiple features using NCBI's e-utilities?
... Many thanks, this looks pretty good. ...
written 4 weeks ago by ThePresident90
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Comment: C: Extracting multiple features using NCBI's e-utilities?
... It's a good start, I can at least have the start/stop positions, the strand and nucleotide accession. One thing that would be really useful is a locus_tag. Thanks, this is still pretty good though. TP ...
written 4 weeks ago by ThePresident90
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Extracting multiple features using NCBI's e-utilities?
... I have a list of protein accession identifiers such as "CBE06962.1". I would like to automatically extract several features such as locus_tag, start and stop positions of the corresponding genes, UniProt tags etc. Is it possible to do it with by combining `esearch` and `efetch` from `e-utilities`, s ...
perl e-utilities written 4 weeks ago by ThePresident90
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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 5 months ago by ThePresident90
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Comment: C: Copy number variation using HTSeq/DESeq2
... I will, thank you for the advice. ...
written 5 months 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 5 months ago by ThePresident90 • updated 5 months ago by WouterDeCoster28k
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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 7 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 7 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 7 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 7 months ago by ThePresident90

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Popular Question 4 weeks ago, created a question with more than 1,000 views. For bowtie --fr/--rf/--ff reporting
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Popular Question 3 months ago, created a question with more than 1,000 views. For Extract soft-clipped reads from BWA -generated SAM file
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