-
Hi~
when I ran the following command :
**tombo resquiggle "/home/weir/output/workspace/pass/1/" "/home/weir/genome/Homo_sapiens.GRCh38.dna.primary_assembly.fa" --processes 4
such errors …
-
Can I omit this parameter when running `STAR alignReads`?
[--outFilterType BySJout](https://github.com/julienrichardalbert/MEA/blob/c33981de99dfd20f76fd5cd904e2f630eef0f4ae/src/scripts/mea.config#L12…
-
Hello Brian,
I'm using the latest release of PASA (2.3) and noticed that the ".valid_gmap_alignments.gff3" file is empty. GMAP seems to have run without a problem, since the "gmap.spliced_alignment…
-
Hi,
Sorry if this is a rather simple question, I am quite new to bioinformatics. I have been running tombo on some RNA sequences and have been trying to perform de novo base detection. After runnin…
-
Tool version 2.1.0 (most current): https://toolshed.g2.bx.psu.edu/view/iuc/hisat2/40e1083a4430
Test history: https://usegalaxy.org/u/jen/h/test-history-hisat2-soft-clip
- Dataset 6: uses all de…
-
"An error occurred setting the metadata for this dataset
Set it manually or retry auto-detection"
I was unable to view spliced alignments produced by TopHat
https://usegalaxy.org/u/amt5284/h/final-…
-
reported by @TKlingstrom
Server error while importing following workflow to test.galaxyproject.org
corresponding sentry entry: https://sentry.galaxyproject.org/sentry/test/issues/290644/
https…
-
Hi, Thank you for developing the tools. I am wondering if it can be used for phasing plant genomes?By the way, I have got pacbio reads and illumina reads, can I get phased_snps.vcf only by these t…
-
Hi,
I am using mashmap with a small testing example as a start. My reference containing 100 sequences and query containing 5 sequences, and the query is exactly the first 5 sequences of the referen…
-
Hi, I was trying to add the sequence to the sam file using my fasta files, but I get an error. I already check that all paths are ok and actually I can see that It gives me a outputfile but with 2 seq…