km-2021

create index failed

10

Hello, I tried to create index, however, the process has failed at the stage to get transcripts.fa. The command and log is as follows: :~$ createindex.cwl https://raw.githubusercontent.com/yyoshiaki/VIRTUS/master/workflow/createindex.job.yaml INFO /usr/bin/cwltool 2.0.20200224214940...

At the Using jellyfish stage of krakenuniq-buid, it dumps core with jellyfish count. Can you please provide a solution? The krakenuniq-build command is the default.

Hi, I am writing to you today to ask a question about FusionCatcher. If FusionCatcher is installed in a conda environment, is the build data for the run directory human_v102?...

I analyzed the report of KrakenUniq using Krona, but I found that some taxonomy IDs could not be found in the local database. I would appreciate it if you could...

Concermong about Normal reference

1

To what extent does the gender bias in a normal reference with 10 cases affect the study's results?

Issue connecting to GitLab server

10

I am writing to you today to let you know about an issue connecting to your GitLab server. I am using the superFreq R pipeline to connect to your server,...

Question about superFreq copy number call output

1

Is there a file that specifies the start and end gene positions of the LOSS or GAIN regions of the copy number call of superFreq?

Is it possible to track which subclones contain a specific genetic mutation in a superFreq riverplot?

1

Is it possible to track which subclones contain a specific genetic mutation in a superFreq riverplot? I am currently using superFreq to analyze a dataset of cancer genomes. I am...

Loaderror

3

Hi, I am experiencing a problem when running the CATT Docker image. The test sample runs fine, but other .fq files fail at the Aligning stage with a LoadError. The...

Hi, Am I understanding correctly that the query.fasta file is the sequence file to be analyzed? Or is it some kind of reference file?