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Forum: Bioinformatics 04-23-2012, 04:16 AM
Replies: 3
Views: 1,864
Posted By qnc
Looking at other threads it might be a fire wall...

Looking at other threads it might be a fire wall problem.

Is there any other site to host BAM and other large files on?

One without download restrictions?

Will check on the UCL Firewall...
Forum: Bioinformatics 04-23-2012, 03:58 AM
Replies: 3
Views: 1,864
Posted By qnc
Trouble UpLoading BAM file to Galaxy

Hi I have been trying to upload this bam file

http://slm22.ioo.ucl.ac.uk/~qncwork/Vanita-Ori.bam

Which is located on this page
http://slm22.ioo.ucl.ac.uk/~qncwork/

All I get is:...
Forum: Bioinformatics 03-23-2012, 10:08 AM
Replies: 16
Views: 3,892
Posted By qnc
This is great advice guys. Thanks will let you...

This is great advice guys. Thanks will let you know how I get on.
Forum: Bioinformatics 03-22-2012, 11:00 AM
Replies: 16
Views: 3,892
Posted By qnc
Cool it works but not quite!!! LOL ...

Cool it works but not quite!!!

LOL

prompt>export PATH=$PATH:/Developer/usr/bin
prompt>make
make: *** No targets specified and no makefile found. Stop.

How do I edit the .bashrc file can I...
Forum: Bioinformatics 03-22-2012, 05:06 AM
Replies: 16
Views: 3,892
Posted By qnc
I get prompt> echo $PATH ...

I get

prompt> echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin

also in /Developer/usr/bin
prompt> ls -F
BuildStrings* dsymutil* mdcheckschema*...
Forum: Bioinformatics 03-22-2012, 04:48 AM
Replies: 16
Views: 3,892
Posted By qnc
Ace! in the bwa folder it has: ...

Ace!

in the bwa folder it has:
COPYING bwa.1 bwt.h bwtgap.c bwtsw2_aux.c khash.h main.c stdaln.h
ChangeLog bwa.txt bwt_gen bwtgap.h bwtsw2_chain.c kseq.h main.h utils.c...
Forum: Bioinformatics 03-22-2012, 04:35 AM
Replies: 16
Views: 3,892
Posted By qnc
Got this error message during install will it...

Got this error message during install will it cause problems?

The system extension “/System/Library/Extensions/hpPlugInInit.kext” was installed improperly and cannot be used. Please try...
Forum: Bioinformatics 03-22-2012, 03:47 AM
Replies: 7
Views: 2,325
Posted By qnc
Got some advice from this thread and so giving...

Got some advice from this thread and so giving that a go. (http://seqanswers.com/forums/showthread.php?p=68420#post68420)

I think I'll get a proper unix installed as well. no harm in having that...
Forum: Bioinformatics 03-22-2012, 03:44 AM
Replies: 16
Views: 3,892
Posted By qnc
Awesome downloading now. :)

Awesome downloading now. :)
Forum: Bioinformatics 03-21-2012, 11:18 AM
Replies: 7
Views: 2,325
Posted By qnc
Thanks guys so what should I do is there another...

Thanks guys so what should I do is there another terminal I can use or do I reinstall it.

How hard is it to turn a PC into linux etc?
Forum: Bioinformatics 03-21-2012, 11:12 AM
Replies: 16
Views: 3,892
Posted By qnc
I upgraded to OSX Lion do you think that could...

I upgraded to OSX Lion do you think that could cause it.

How do I set a path to see if the make works again or where is the make directory likely to be so that I can test it in that folder to see...
Forum: Bioinformatics 03-21-2012, 10:24 AM
Replies: 7
Views: 2,325
Posted By qnc
Mac OSX Lion Terminal Version 2.2.2 (303) Problems

Hi,

The genomeCoverageBed program made each line without the "Chr" start making it hard to use in UCSC Genome browser.

i.e.
17 422997 422999 26
17 422999 423001 27
17 423001 423003 29
Forum: Bioinformatics 03-21-2012, 10:12 AM
Replies: 16
Views: 3,892
Posted By qnc
SAM tools on a mac

Hi,

I have tried to down load and instal SAMTools on my mac to make VCF files from a BAM file I have but it is not working?

What I did:
I tried to follow these instructions here...
Forum: Bioinformatics 01-23-2012, 10:08 AM
Replies: 14
Views: 6,518
Posted By qnc
Smile This from this post...

This from this post (http://seqanswers.com/forums/showthread.php?p=53955)

might help with making it Wiggle Format. I haven't tried so I'll leave the advice as I got it.



Hope that helps...
Forum: Bioinformatics 01-23-2012, 09:32 AM
Replies: 14
Views: 6,518
Posted By qnc
HI SEQond, Here is what I found so far ...

HI SEQond,

Here is what I found so far

A MINI GUIDE TO MAKING A HISTOGRAM FOR COVERAGE OF NEXT GEN SEQ DATA ON UCSC GEMONE BROWSER

There are 3 parts to this mini guide: 1) Required files,...
Forum: Bioinformatics 12-13-2011, 08:20 AM
Replies: 14
Views: 6,518
Posted By qnc
I can see what I can do to help I'm no expert....

I can see what I can do to help I'm no expert. What are you having trouble with?
Forum: Bioinformatics 10-25-2011, 08:06 AM
Replies: 14
Views: 6,518
Posted By qnc
Awesome got it working its the header which is...

Awesome got it working its the header which is wrong some where probably browser position?

LOL on to the next challenge.
Forum: Bioinformatics 10-25-2011, 06:58 AM
Replies: 14
Views: 6,518
Posted By qnc
Thanks for that removed the "" that I had but...

Thanks for that removed the "" that I had but still getting an error message from UCSC

Error line 1 of var browser position chr22:1-51,304,566 in custom input: type=bedGraph name=CoverageHistogram...
Forum: Bioinformatics 10-25-2011, 04:42 AM
Replies: 14
Views: 6,518
Posted By qnc
UCSC histogram view

Thanks to USers arvid, GenoMax & dpryan I managed to get

$ ./genomeCoverageBed -ibam test.bam -g human.hg19.genome -bg > testBamHisto.BedGraph

to produce a file for UCSC which has this kind of...
Forum: Bioinformatics 10-25-2011, 04:30 AM
Replies: 4
Views: 4,746
Posted By qnc
LOL Ok it has made the file now I'll need to ask...

LOL Ok it has made the file now I'll need to ask a UCSC expert about the look of it.

Wanted the Histogram view rather than the actual numbers?

More research required but thanks, learning a lot...
Forum: Bioinformatics 10-25-2011, 04:04 AM
Replies: 4
Views: 4,746
Posted By qnc
Thanks its is working now But how do I get a...

Thanks its is working now But how do I get a report from its run that can be loaded into UCSC as a histogram track so I can see the coverage of the BAM file.

I tried this but it didn't work?

...
Forum: Bioinformatics 10-24-2011, 07:00 AM
Replies: 4
Views: 4,746
Posted By qnc
Genome files for BEDTools GenomeCoverage command

Hi trying to get the BEDTools genomeCoverage working


$ ./genomeCoverageBed -i test.bam -g human.hg19.genome
It looks as though you have less than 3 columns at line: 1. Are you sure your files...
Forum: Bioinformatics 10-21-2011, 10:11 AM
Replies: 27
Views: 12,570
Posted By qnc
Awesome!!! $ ./intersectBed -a less.bed...

Awesome!!!


$ ./intersectBed -a less.bed -b more.bed
chr6 112879106 112879267 D6S474 1000 + 112879106 1chr69267119553773,0,0, 119553939 D6S287-L-5-18 1000 + 11955377chr6 ...
Forum: Bioinformatics 10-21-2011, 08:38 AM
Replies: 27
Views: 12,570
Posted By qnc
Unhappy Ok it seems to have worked... but is still not...

Ok it seems to have worked... but is still not working?

here is the bin now with the programs and two small bed files (less.bed & more.bed) just to see if it is working but I get the following...
Forum: Bioinformatics 10-21-2011, 08:24 AM
Replies: 27
Views: 12,570
Posted By qnc
Ok will retry the complie and let you know. ...

Ok will retry the complie and let you know.

If I get any errors I'll post them up here.
Showing results 1 to 25 of 51

 


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