The .bigwig files I make and upload to Galaxy get a "Display on UCSC browser" link. Another person in my lab made .bam files from Tophat using Galaxy and also has the Display on UCSC link. When I make .bam files on my own computer and upload them to Galaxy there's no Display on UCSC link. How can I display .bam files that I make myself (from Tophat) and upload to Galaxy on the UCSC browser? I tried uploading a .bai file as well but that didn't help.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
The .bam files are up to 10 GB so a bed file would be huge, so would take a long time to upload and only small portions could be displayed at a time (500MB upload limit to UCSC). I could ultimately make a .bigbed file which I assume could be displayed from Galaxy to UCSC as I had no problems with .bigwig files but the idea is to have a relatively quick way to visualize the Tophat output in the UCSC browser.
Comment
-
My guess is that Galaxy is not recognizing it as a BAM file (in which case change the datatype), or it is not sorted, in which case try sorting it. I think. :-)
Could also post to galaxy-user list. Subscribe here: http://lists.bx.psu.edu/listinfo/galaxy-user
Comment
Latest Articles
Collapse
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
30 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
32 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
28 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
52 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment