Forum
RNA edition
Hi, any experience bringing REDItools (<https://github.com/BioinfoUNIBA/REDItools>) as a Seven Bridges app?, thanks
Posted by Ricardo Armisen about 2 months ago
Problem with File upload
How do I fix this error with sb?
sb: <ERROR> Cannot communicate to the server
The web interface is too slow for 2 GB fastq.gz files, so I triesd the sb utility and got the error message above
Posted by Rick Jensen 4 months ago
Linebreak in Project Wiki Markdown?
Hi,
How can I insert a linebreak/newline in a Project Wiki?
For example, the default Description of a project contains vertical whitespace between paragraph, as in:
"After reviewing the information above, you can continue to use this space for adding notes about your project such as its aims, experimental context, and any other ideas that you’d like to share with your project members as everyone will see the same content. You can also use markdown here to add formatting to your notes.
To start adding your description, click Add Description below.
Remember that details of each pipeline execution you run on the Seven Bridges Platform are logged on the dedicated task page."
How can I replicate that? I have read the markdown demo (https://markdown-it.github.io/) linked from the project description, but see no mention of linebreaks or vertical whitespace.
Thank you,
Brian
Posted by Brian White 6 months ago
TCGA diagnostic slides - stain types
I'm working on a research project that involves the analysis of MSI/MSS status in H&E stained diagnostic slides from the COAD and READ cohort in the TCGA database. I've collected around 600 slides so far, but I've encountered some difficulties in finding information about the staining procedure used.
While most of the slides appear to have been stained using the standard H&E stain, some of the slides seem to be stained differently, with a more purple/blue hue.
Is this information about the staining procedure available in the TCGA database?
Are there any tools (like a python package or something) that could identify the stain type from the diagnostic slide?
Any suggestions or advice would be greatly appreciated.
Thanks
Posted by Sharon Peled 8 months ago
Different instance types for different workflow steps?
Is it possible to have different steps in a workflow run on different instance types? Or is it always just the single instance type?
I have a pipeline that contains some single threaded steps, like biobambam bamtofastq, and some that are multithreaded, like bowtie2 and samtools sort. Seems like a waste of resources to run a c4.2xlarge for a single thread. And a bit more cumbersome to have to run the pipeline in different steps and manually cleanup.
Posted by Jake Wendt 8 months ago
Search filename in the GDC data portal
Hi,
3 years ago I downloaded tsv files of indels and SNVs of TCGA samples from the GDC data portal.
Right now I want to find the barcode-id of each sample.
When I search for the specific file names in the GDC there is no result.
An SNV file name for example:
c84b676a-a409-517f-9920-b63119f1f717
An Indels file name for example:
067a20c4-a4da-5899-810f-5768d0a43555
Does anyone have a solution?
Thanks!
Posted by Oriya 10 months ago
Can you transfer files from CGC to GEO?
Can you transfer files from CGC to GEO?
Posted by Rocio T Martinez-Nunez about 1 year ago
GRAF benchmarking
Hey!
Hope you're well! We ran the GRAF pipeline for NA12878 with this inputs and take the ouput and ran hap.py comparing the results with the gold standard downloaded from this link: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/latest/GRCh38/ and obtain: 56.42 % of precision for all indels and 84.01% of precision for all snps. Based on the publication of GRAF and what we've seen on the blog, the expected precision was near 99% but we are not being able to reproduce these results. Do you know what could be wrong? Thanks in advance for your help!
Best,
Maria Teresita Laguinge
Posted by Maria Teresita Laguinge about 1 year ago
Problem of permissions executing a tool
I'm running a tool that uses perl and python scripts, when I ran the tool, I get an error of permission: 2022-08-06T17:55:11.440911533Z Can't exec "annotate_variation.pl": Permission denied at /sbgenomics/workspaces/94457834-7ccb-45da-84c3-ee44297388a4/tasks/f9019512-ba43-4ff9-9839-889e8cbf3290/intervar_cwl/table_annovar.pl line 444.
Do you know why this could be and how to fix it?
Posted by Maria Teresita Laguinge about 1 year ago
I can't view the Mouse reference genome in the Genome Browser
I have been trying to view the aligned files in the genome browser but I am not able to view the mouse mm10 reference genome.
It gives this as the error:
Unable to recognize genome reference from the BAM header. Using Human hg19.
Posted by Shwetal Talele over 1 year ago