-
Is my alignment file wrong? QoRTs.jar was executed in windows platform.
E:\junse>java -jar QoRTs.jar QC SAMP1.bam Bom7.gtf /output/
Starting QoRTs v1.2.42 (Compiled Fri Jun 2 12:23:55 EDT 2017…
-
Hi @tomasbruna,
I ran Braker to predict gene structure and got the problem in the step running Genmark-EX as below.
I used the reference genome and customized amino acid sequence database with t…
-
Hi,
I recently ran into a very rare bug where I added U1,U2,U3,U4,U5,U6 and other snoRNAs to the genome and then defaulted the parameters to build the index. Then map my data on it. Then the program …
-
Hi,
I am mapping my Ribo-seq data, which are very short(about 30nt), to my reference. Here is my command:
```
STAR --runMode alignReads \
--runThreadN $t \
--genomeDir ${mhSTARindex} \
--re…
-
Hi, I noticed some strange behavior when running HISAT2 (v 2.1.0) on many files at once. Some background: The data I'm working with are from 2 flow cells (fcA/B), 4 lanes each(L001/2/3/4), paired end,…
-
Hello,
I wanted to download Splice Junction files for the Primary Tumors of the TCGA-GBM project. I am runnin g R 4.0.0.
I used the command
`query The columns of the SJ.out.tab file have the follo…
-
Is it possible to use PhyloCSF on mitochondrial genomes, i.e. with an alternative genetic code?
-
I am running ProtHint on a plant genome with a set of plant proteins. After a day with things running well until the step : " predict final gene set"
I get this error message:
error, file not foun…
-
Hi- I seem to be unable to make spaln work even in the most basic case. I would appreciate any guidance. This is using spaln 2.4.9 installed via bioconda. My final aim is to align proteins or cDNA fro…
-
Hello everyone! This is my first time analyzing RNAseq data and I am very much learning as I go while following a YouTube series (https://www.youtube.com/watch?v=butxOf_fxTY&t=217s&ab_channel=SimonCoc…