On Fri, Jul 6, 2012 at 3:07 AM, Aarti Desai
wrote:
> These show up in the history with the appropriate size. But when I choose
> the “Map with BWA for Illumina” option, the two fastq files do not show up
> in the FASTQ file drop down.
Hi Aarti,
Most tools in galaxy that work with fastq file need
Hello,
Using the defaults and then testing the resulting SAM output seems to be
what most folks are doing if they do not have access to the original
library construction methods (e.g. size selection). Both SAM Tools and
Picard are in Galaxy. This is a useful post where the options are discuss
Hi all,
I am a new Galaxy user and I have searched the mail list, looking for the
answers to my questions, but failed.
I am trying to fetch the corresponding codon or amino acid alignments among 46
species using genomic intervals in human.
I know if I have a list of human genomic intervals, I
I used SICR to call peaks and have following out put files:
1. test.1removed bed
2. control1 removed .bed
3. test w 200 graph
4. test w200 normalized graph
5. test w200-G600 FDR.05 island.bed
6. test w200-G600 FDR .05 island filtered.bed
7. test w200-G600 FDR .05 island filtered normalized.wig
8
Hi Patricia,
If your data is still in MAF format, first convert it to FASTA using the
tool "Convert Formats -> MAF to FASTA". Next, translate the regions
using the tool "EMBOSS -> transeq".
Depending on where your intervals are located, the data may get
confusing at the translation step if y
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