User: ThePresident

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ThePresident90
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Posts by ThePresident

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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 weeks 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 weeks 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 weeks 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 6 weeks 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 6 weeks 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 6 weeks ago by ThePresident90 • updated 6 weeks ago by Kevin Blighe6.8k
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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 12 weeks ago by ThePresident90
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Comment: C: How to extract only 5-prime hard/soft clipped reads?
... You're right. I am just unsure for which flag I should filter (all these extracted reads are flagged either as 147, 163, 99 or 83). I'm currently looking at this, but if you have a suggestion, go ahead. Thanks for pointing out this detail. ...
written 12 weeks ago by ThePresident90
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Answer: A: How to extract only 5-prime hard/soft clipped reads?
... I couldn't figure out how to get this using pysam, but I might have found another solution using simple `awk` awk -Ft '$6 ~ /^..?S/ {print $2, $4, $9}' input.sam > output.txt This will extract columns 2,4,9 from the SAM file whenever character S (used to mark soft clipped nucleotides in th ...
written 3 months ago by ThePresident90
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Comment: C: How to extract only 5-prime hard/soft clipped reads?
... Already tried: > >pip install pysam Requirement already satisfied: pysam in ./Documents/Tools/HTSeq-0.9.1/.eggs/pysam-0.11.2.2-py2.7-macosx-10.6-intel.egg But I've figured out another way around my problem using `awk` (see below). Eventually, I'll have to figure out this pysam problem since ...
written 3 months ago by ThePresident90

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