User: ersgupta

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ersgupta0
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Posts by ersgupta

<prev • 7 results • page 1 of 1 • next >
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difference between mummer --mum and delta-filter -r -q
... I want to run genome-genome alignment using nucmer. The plan was to do nucmer with --maxmatch (takes very long) and then do delta-filter to retain 1-1 alignments. My question is, if I run nucmer with --mum option, isn't that same as applying delta-filter 1-1 on maxmatch output? Am I missing somethi ...
genome alignment mummer alignment nucmer written 23 months ago by ersgupta0
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Comment: C: plotting GO enrichment pvalue
... I agree, ggplot2 is quite flexible, will give it a try. Thanks. (y) ...
written 4.3 years ago by ersgupta0
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Comment: C: plotting GO enrichment pvalue
... Ah, I have uploaded the image for the first time in biostars, so might not have done it right. Thanks genomax2 for fixing it. :) ...
written 4.3 years ago by ersgupta0
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Comment: C: plotting GO enrichment pvalue
... Thank you so much for the reply. Will try out using Inkspace and maybe gimp as well, didn't really want to go manual, was wondering if this "trivial" thing can be achieved with just the script, like moving the yaxis to the middle or something. GeneSCF looks pretty good, haven't tried it before, but ...
written 4.3 years ago by ersgupta0
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plotting GO enrichment pvalue
... I want to plot horizontal barplot for -log(pvalue) from goseq output. Till now I have been able to plot this(http://e18i.imgup.net/testc1e0.jpeg ), using barplot() in R. barplot(values, horiz=T, names.arg=names, las=1, cex.names=0.6) but it cuts out the labels on the y-axis, is there any way i ...
histogram rna-seq go goseq written 4.3 years ago by ersgupta0 • updated 4.3 years ago by WouterDeCoster44k
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Comment: C: Creating alternate Bed file by incorporating INDELs locations
... Yeah, was planning to do that. But just thought to ask if anyone already has a script for this. It would be great if there was something like FastaAlternateReferenceMaker for bed files, I guess will have to write on my own. ...
written 5.2 years ago by ersgupta0
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Creating alternate Bed file by incorporating INDELs locations
... I have a exome bed file (coordinates wrt to ref genome) and a bed file with coordinates of INDELs (incorporated in ref genome). Now I want to generate a modified exome bed file which can shift the coordinates wrt to INDEL event. For. eg.  exome bed file: chr1 10 100 chr1 200 400 indels file: chr ...
sequence sequencing written 5.2 years ago by ersgupta0

Latest awards to ersgupta

Popular Question 21 months ago, created a question with more than 1,000 views. For Creating alternate Bed file by incorporating INDELs locations
Popular Question 4.2 years ago, created a question with more than 1,000 views. For plotting GO enrichment pvalue

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