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Question: how to map and duplicate using the web-based Galaxy
0
gravatar for xujiean66
4.1 years ago by
xujiean66 • 0
China
xujiean66 • 0 wrote:

hello,i am grateful for your answers.

I have two questions,

First,before i do map fastq to fasta,whether i could do bwa index for fasta,or the "mapping with BWA "in tool pane is got ready in the "mapping with BWA" software package.

Second,i can not find "sortsam"in Picard tool pane when i do according procedure"mark duplicate",how can i do next step? whether any other tool could instead of "sortsam",or whether any other workflow i can finish the DNAseq all using tools in web-based Galaxy?

Thanks!

 
dnaseq • 865 views
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modified 4.1 years ago • written 4.1 years ago by xujiean66 • 0
0
gravatar for Jennifer Hillman Jackson
4.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

For the first, it is not necessary to do any indexing if you are using a custom reference genome. Just load it as fasta into your history as a dataset and use that.

SAMtools sort is not on the public Main Galaxy instance at http://usegalaxy.org. For sorting SAM/BAM files, try the Picard reorder tool or a workflow such as this (this and other variations are under "Shared Data -> Published Workflows", or you can import and edit as you wish): 
http://usegalaxy.org/u/jen-bx-galaxy-edu/w/sort-bam-inc-headers

A ticket to add the tool to Main exists here (but is still under consideration): https://trello.com/c/PxiesIK6

If you want to use the tool in a local or cloud Galaxy, it can be found in the tool shed. http://usegalaxy.org/toolshed

Hopefully this helps, Jen, Galaxy team

 
ADD COMMENT • link written 4.1 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for xujiean66
4.1 years ago by
xujiean66 • 0
China
xujiean66 • 0 wrote:

Thank you very much！I have finished my work.
ADD COMMENT • link written 4.1 years ago by xujiean66 • 0
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