Re: [galaxy-user] Convert SOLiD data

2011-03-28 Thread Jennifer Jackson
onday, March 28, 2011 9:57 AM To: lishiyong Cc: galaxy-user Subject: Re: [galaxy-user] Convert SOLiD data Hello Lishiyong, Just to confirm, the conversion was performed at Galaxy main using "NGS: QC and manipulation -> Convert SOLiD output to fastq"? With the option "double en

Re: [galaxy-user] Convert SOLiD data

2011-03-28 Thread Peter Cock
On Mon, Mar 28, 2011 at 3:11 PM, Sher, Falak wrote: > My second question is, > 2) How can I convert SAM/BAM formated files (generated by Bowtie > mapping tool at Galaxy) to Wiggle or Bigwig formats. Brad Chapman has written a Galaxy tool for converting BAM to BigWig, called "Calculates coverage fr

Re: [galaxy-user] Convert SOLiD data

2011-03-28 Thread Sher, Falak
: galaxy-user Subject: Re: [galaxy-user] Convert SOLiD data Hello Lishiyong, Just to confirm, the conversion was performed at Galaxy main using "NGS: QC and manipulation -> Convert SOLiD output to fastq"? With the option "double encode = yes"? If so, the output appears to be co

Re: [galaxy-user] Convert SOLiD data

2011-03-28 Thread Jennifer Jackson
Hello Lishiyong, Just to confirm, the conversion was performed at Galaxy main using "NGS: QC and manipulation -> Convert SOLiD output to fastq"? With the option "double encode = yes"? If so, the output appears to be correct. quote from tool help: "Double encode? - converts color calls (0123.

Re: [galaxy-user] Convert SOLiD data

2011-03-28 Thread Ryan Golhar
Lishiyong, You should not convert colorspace to base space prior to aligning reads. The reason for this is that if there is an error in one of the color calls, it will effect all the downstream color calls. Instead, you should use an aligner that will do the assembly in color-space instead.