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Forum: Bioinformatics 02-27-2013, 11:17 PM
Replies: 1
Views: 1,817
Posted By adrianl
PATH...

PATH (http://en.wikipedia.org/wiki/PATH_(variable)) is a variable containing information on the directories that contain executable programs. If you type echo $PATH into your shell, it will spit the...
Forum: Bioinformatics 01-24-2013, 11:13 PM
Replies: 3
Views: 1,271
Posted By adrianl
http://seqanswers.com/forums/showthread.php?t=2433...

http://seqanswers.com/forums/showthread.php?t=24331

I think this thread concerns the same question
//A
Forum: Bioinformatics 01-18-2013, 05:19 AM
Replies: 4
Views: 1,285
Posted By adrianl
I think so too. If you are interested in making...

I think so too. If you are interested in making plots like these yourself I suggest taking a look at the ggplot2 (http://ggplot2.org/) package that is available for R. It removes some of the...
Forum: Bioinformatics 09-25-2012, 04:02 AM
Replies: 4
Views: 1,985
Posted By adrianl
Smile Thank you Graham, for your input! I ran...

Thank you Graham, for your input!

I ran readcounts with parameters:
--min-coverage 0
--min-base-qual 30 (Since this is what I ran mpileup2idel with)

And I think I found the answer to my...
Forum: Bioinformatics 09-24-2012, 02:50 AM
Replies: 4
Views: 1,985
Posted By adrianl
Varscan frequency question

I've been trying out varscan for indel calling recently but I have an issue with the output, rather the information in the output... The field named Freq doesnt seem to agree with the different Reads...
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