Skip to content

issues Search Results · repo:igordot/sns language:Shell

Filter by

14 results
 (72 ms)

14 results

inigordot/sns (press backspace or delete to remove)

igordot/sns
Problem with differential expression analysis

Hey Igor, I am doing differential expression analysis on some DNA sequences, and I had some trouble with the sns/run rna-star-groups-dge command as it does not output any r data files or graphs for me ...
  • adaminjoon
  • 14
  • Opened 
    on Aug 10, 2023
  • #15

igordot/sns
Question Regarding PCA plot

Hi Igor, Was wondering how can i set assign each group when running rna-star-groups-dge a specific color ? I have only two groups and I would like to choose which is red and which is blue on the PCA Thank ...
  • Miladebrahim
  • 1
  • Opened 
    on Aug 8, 2023
  • #14

igordot/sns
fastq

hi igor, im trying to run a wes for one sample that was processed by azenta...i uploaded all the required docs for the run and i am getting this error: [torunp01@bigpurple-ln3 twofortyeight]$ sns/run ...
  • ptoru001
  • 2
  • Opened 
    on Mar 27, 2023
  • #13

igordot/sns
Sample_groups_for_RNA_STAR_route

Hi Igor, How can i define the group that i need to compare to a control (i.e. if i assign the samples as Xmutant and Xwildtype, the results come back comparing Xwildtype to Xmutant) how can i reverse ...
  • Miladebrahim
  • 9
  • Opened 
    on Oct 5, 2022
  • #12

igordot/sns
question

Hi, this is not really an issue but more of a question. For the normalized counts ouput, is it in RPKM?
  • mannekim
  • 1
  • Opened 
    on Sep 26, 2022
  • #11

igordot/sns
ERROR: the value for setting EXP-TARGETS-BED must be specified logs-sbatch/slurm-18641451.out: qc-target-reads-gatk.sh ERROR: BED DOES NOT EXIST

Good morming Igor, I have 7 samples 5 normal and two tumor. The bed file has already bee added and is the same one as I used last time. -rwx------ 1 torunp01 hackerlab 11302942 Jul 7 12:12 TruSeq_Exome_TargetedRegions_v1.2.bed ...
  • ptoru001
  • 14
  • Opened 
    on Aug 23, 2022
  • #9

igordot/sns
exitcode1 by slurm

Good Afternoon, I am getting this error: Slurm Job_id=17749799 Name=sns.wes.ptm1__214518 Failed, Run time 00:00:02, FAILED, ExitCode 1 eventhough I have added the reference bed file for the sequence ...
  • ptoru001
  • 16
  • Opened 
    on Jul 5, 2022
  • #8

igordot/sns
newbie

HI All, I have just run a sns/wes and a little confused of what to do next.... i am in the folder where i see : samples.fastq-raw.csv sns logs-sbatch samples.fastq-clean.csv settings.txt summary FASTQ-CLEAN ...
  • ptoru001
  • 12
  • Opened 
    on Jul 1, 2022
  • #7

igordot/sns
access to genome dir?

Hello! I m having a small issue with the ChIP seq peak calling. The first ChIP route worked great. I m in the same folder and manually edited the samples.pairs.csv with IPs and inputs. I ve updated the ...
  • lgoehring
  • 8
  • Opened 
    on Jun 22, 2022
  • #6

igordot/sns
errors in wes-pairs-cnv pipeline

When trying to run the wes-pairs-cnv pipeline, I get the following errors: logs-qsub/sns.wes-pairs-cnv.SeraCare-1to4-Positive-HapMap-B17-1267.o3950853: get-set-setting.sh ERROR: the value for setting ...
  • stevekm
  • 5
  • Opened 
    on Oct 25, 2017
  • #5
Issue origami icon

Learn how you can use GitHub Issues to plan and track your work.

Save views for sprints, backlogs, teams, or releases. Rank, sort, and filter issues to suit the occasion. The possibilities are endless.Learn more about GitHub Issues
ProTip! 
Restrict your search to the title by using the in:title qualifier.
Issue origami icon

Learn how you can use GitHub Issues to plan and track your work.

Save views for sprints, backlogs, teams, or releases. Rank, sort, and filter issues to suit the occasion. The possibilities are endless.Learn more about GitHub Issues
ProTip! 
Press the
/
key to activate the search input again and adjust your query.
Issue search results · GitHub