Question: Source fasta sequence options unavailable
0
gravatar for devbt15
19 days ago by
devbt1530
devbt1530 wrote:

Dear all,

While trying to use the data manager for hisat2 index building, I do not get any dropdown options for the source fasta sequence, although I have uploaded the genome.fasta file to my data on local galaxy. I also tried the NormalizeFasta command from picard tool on the genome.fasta file but the output fasta file is also not available in the hisat2 index tool. Please help.

Regards,

Debatosh Das.

ADD COMMENTlink modified 15 days ago by Jennifer Hillman Jackson23k • written 19 days ago by devbt1530
1
gravatar for Jennifer Hillman Jackson
15 days ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

My guess is that you still need to run the "Fetch genome and create dbkey" data manager first, then Samtools, followed by Picard. After that, any of the others can be run on the fetched genomes as these will now appear in the drop-down menu. The data managers for mapping tool indexes will not have any selectable content until a genome is fetched and initialized.

Run the data managers in the order explained in this prior post and watch the linked video tutorial for even more help: https://biostar.usegalaxy.org/p/21749/

Thanks! Jen, Galaxy team

ADD COMMENTlink written 15 days ago by Jennifer Hillman Jackson23k
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