-
Hi, I run the PASA in docker, when using the "/usr/local/src/PASApipeline/scripts/build_comprehensive_transcriptome.dbi" tools with the defaults parameters, however, this error appeared.
Limited err…
-
Hello, I hope you're well!
### Context
1. I performed short-read (Illumina, 150bp PE) and long-read (ONT, cDNA+PCR) RNA-sequencing on 12 human cell line samples (4 conditions, 3 biological repli…
-
Currently, objectives are run for the output of every target run. In some use cases (e.g. transcriptome assembly), multiple different parameter sets will result in exactly the same assembly. Let's tak…
-
Hi,
we just received an MAS-Iso seq long read data for single cell 3'p for test which I am trying to process as per the Longbow pipeline , the bam file from the longbow output is giving an erro…
-
Hi again,
For Braker1, I had been providing BAM files produced by STAR.
Since you are now using StringTie assembly as part of the Braker pipeline, I was wondering if there are any notable perfo…
-
Hi,
I'm having issues generating a standard nr kraken2 database + a few local fasta files.
I have generated a database on this system before without issues, so presumably it may result from some…
-
I am running find_enrichment.py of a Denovo transcriptome assembly, and I want to have it as a description of the GO abundance in my nonmodel plant transcriptome. Given that my IDs are unknown, I cr…
-
Dear Brian,
I try to assembly my metatranscriptomic paired end library, if the command:
Trinity --seqType fq \
--max_memory 80G \
--left ../clean_data/SRR3089571_1.fastq \
--right ../…
-
Hi there,
I need to convert the headers in my Trinity.fasta file that look like this:
>TRINITY_DN73_c0_g1_i1 len=203 path=[1:0-141 120:142-202] [-1, 1, 120, -2]
Into headers that are contig00…
-
Hi friends!
I runned metaWRAP quant_bins without any errors, but I entered 808 bins and ended up with only 7 bins in bin_abundance_table.tab, I don't know why, and hope you can answer, thank you v…