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Search: Posts Made By: Ka123$
Forum: Bioinformatics 10-09-2009, 11:45 AM
Replies: 236
Views: 587,009
Posted By Ka123$
Hi apfejes, I had sent you my email ID earlier...

Hi apfejes,
I had sent you my email ID earlier last week. I was wondering if you got it or not....Please can you check again. I am sending you a email with this thread and you can reply to me on...
Forum: Bioinformatics 09-30-2009, 04:59 PM
Replies: 236
Views: 587,009
Posted By Ka123$
Thanks so much anthony ! If you could compile and...

Thanks so much anthony ! If you could compile and email me that will be great!!!! I appreciate it so much!.......
Forum: Bioinformatics 09-30-2009, 04:31 PM
Replies: 236
Views: 587,009
Posted By Ka123$
Hi Anthony, so here is what I am doing. We have...

Hi Anthony,
so here is what I am doing. We have decided to stick with the GERALD files to convert it to wig.......(PI's order !)
I checked for unaligned files and none were there.
I have a .export...
Forum: Bioinformatics 09-30-2009, 03:08 PM
Replies: 236
Views: 587,009
Posted By Ka123$
can anyone let me know why findpeaks...

can anyone let me know why findpeaks separatereads.jar command cannot create a log file when I use the GERALD aligned files or the bowtie aligned files?
In GERALD aligned files I indicated elandext...
Forum: Bioinformatics 09-28-2009, 07:49 PM
Replies: 236
Views: 587,009
Posted By Ka123$
First of, thanks so much for all your guidance,...

First of, thanks so much for all your guidance, from both of you!
I really appreciate it so much!

I previously tried using bowtie aligner. As bowtie aligner gave me only one separatefile.gz and I...
Forum: Bioinformatics 09-28-2009, 11:33 AM
Replies: 236
Views: 587,009
Posted By Ka123$
Thanks to both kmcarr and apfejes ! I did...

Thanks to both kmcarr and apfejes !
I did belive that GERALD generates the Eland format files. But when I used GERALD files to perform a separate reads according to findpeaks and I used ELAND as an...
Forum: Bioinformatics 09-28-2009, 04:10 AM
Replies: 236
Views: 587,009
Posted By Ka123$
If I would directly perform separate reads and...

If I would directly perform separate reads and sort reads on the GERALD alignment files what type of aligner do I need to specify? GERALD/Eland if specified give me an error on fndpeaks
Error: ...
Forum: Bioinformatics 09-28-2009, 03:35 AM
Replies: 236
Views: 587,009
Posted By Ka123$
what kind of formats are BUSTARD and GERALD files...

what kind of formats are BUSTARD and GERALD files from solexa?
Forum: Bioinformatics 09-24-2009, 10:27 AM
Replies: 236
Views: 587,009
Posted By Ka123$
Thanks a lot I will try all the options you gave...

Thanks a lot I will try all the options you gave me and let u know how it worked for me.
Forum: Bioinformatics 09-24-2009, 09:57 AM
Replies: 236
Views: 587,009
Posted By Ka123$
sortpeaks

Yeah sure,
I had this huge I human seq reads that I aligned using bowtie. This bowtie alignment I need to convert into wig files. So I have been using the separateReads as the first step in...
Forum: Bioinformatics 09-24-2009, 07:51 AM
Replies: 236
Views: 587,009
Posted By Ka123$
Solexa findpeaks

Using Findpeaks sort reads on bowtie mapped alignment is taking up too much memory......!!!!! So I am trying using the GERALD maps reads directly from solexa to convert to wig files...I believe the...
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