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Old 09-28-2009, 06:49 PM   #193
Location: MD

Join Date: Jul 2009
Posts: 27

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 could not make sense of it.... We reverted to use GERALD alignment directly to separate and sort.........But here are the comands I have used using bowtie aligner:

Secondly I followed bowtie commands to do my alignment .
./bowtie -a -v 2 -f h_X_GERALD.fa h_sap (did I have to use the -chr here???)

I used findpeaks cmds here:
java -jar -SeparateReads.jar elandext p_align_copy p_7_ger

(before I had problems using this for gerald and it said aligner format not recognised,so according to the blog I used elandext
java -jar SeparateReads.ja
r elandext p_align_copy p_7_ger
Error: Couldn't create log file : p_7_ger/SeparateReads.log)

for sort reads previously I have used this cmd:
java -jar Sort* bowtie g_sort_7 p_7_ger/*.bowtie

(although it ran sometime gave me memory problems)
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