Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:1
-
Sprint:Summer 7
Description
IGB can now open and display contents of CRAM files distributed by Nebula Genomics.
AL has a recently downloaded CRAM file from Nebula that would be great to use, but it's huge - around 84 Gb.
For this task, let's use a command line tool to extract the data for chromosome 1, the chromosome shows by default when it opens the latest human genome available in the browser - hg38.
Let's deploy the actual data file on RENCI hosting and add it as a new data set in IGB Quickload main.
Once it is there, we can then create a tutorial and also a video showing how to open and load the reads to look for or sanity-check polymorphisms. The tutorial ought to explain the soft clips and the SNPs - what they are and how to interpret them. The materials could also explain how to visually check some of the SNP calls on the Nebula Web site.
Attachments
Issue Links
- relates to
-
-
- Closed
-
Activity
Following the instructions above, I was able to successfully open the file in IGB and have confirmed that I can load data and load sequence. I've also confirmed that no data is loading in chromosomes other than chromosome 1 as expected.
Ready for next steps!
Attn Nowlan Freese and Paige Kulzer:
This could be reviewed by Nowlan Freese and/or Paige Kulzer.
To review, open the file in IGB and confirm that you can load the data. Please see above for instructions.
Checking uploaded file in IGB:
- Started IGB
- Opened human hg38 genome version H_sapiens_Dec_2013
- Chose File > Open URL and entered URL:
http://lorainelab-quickload.scidas.org/genomesequence/H_sapiens_Dec_2013/M1YNF4X1J.chr1.cram
- Visited chromosome 1, navigated to a gene region, zoomed in, selected "Load Data" and "Load Sequence"
- Made the two attached images showing what appears to be a region where a lot of alignments end or start with gray "soft clip" glyphs. The boundaries of the software clips do not perfectly line up with each other. I do not know how to interpret this, but it seems an interesting pattern.
Trying to deploy file from local Spectrum internet is not going well. Uploading to data.bioviz.org was extra slow: 1+ h for 2 Gb. I had to use the VPN. Maybe sending the upload through the VPN was a problem.
Trying now to upload to RENCI host with:
local aloraine$ scp -J aloraine@hop.renci.org M1YNF4X1J.chr1.cram aloraine@lorainelab-quickload.scidas.org:/projects/igbquickload/lorainelab/www/main/htdocs/genomesequence/H_sapiens_Dec_2013/.
Transfer rate is around 2.2 Mbs
Update:
- Using samtools, I made a new cram file with chromosome 1 data only and made an index for it:
local aloraine$ samtools view --threads 16 -Cho M1YNF4X1J.chr1.cram M1YNF4X1J.cram chr1 local aloraine$ samtools index M1YNF4X1J.chr1.cram
- Checked the header with:
samtools view -H M1YNF4X1J.chr1.cram
I attached the header section (output from above command) as a plain text file. Check out the command "PG" command line ( ? ) tags. You will be shocked!
Question:
- Does IGB keep an in-memory copy of the entire "header section" data for every entry in a CRAM file it has already loaded?
Thank you Paige Kulzer! I think this is all that is needed to do for this ticket. When ready, Nowlan Freese is going to add this to the IGB Quickload main folders for the human genome.
I think that for the next steps, we should re-open the ticket where we made a video / tutorial for the new CRAM feature and re-do the material to focus on individual genome sequencing.
I am going to close this ticket now.