dvirdi01

I have bunch of Oxford long-read fastq files that I need to convert to sorted bam files and later assembly using stringtie. I ran the following command for conversion from...

Inputting multiple long-read files at once

3

All the files I need to run this on are in a directory. Is there a way I can give the path to the directory in -long rather than listing...

RNABloom not creating transcriptome files

3

I ran rnabloom on several of my input files individually. out of my 10 samples, it did not produce any transcriptome file for 2 of them. Why is that? It...

Java out of memory exception

3

I ran bloom on multiple fastq files together by giving it 200GB ram. It gave me out of memory exception mid way. I was running the command using a salloc...

GTF input file

1

It says that SUPPA takes in fastq files and also genome annotation GTF file. By genome annotation does it mean the reference genome gtf file? I assembled my long reads...

i Used the correct command to do splice analysis on my stringtie assembled gtf files. It did not show me the desired output. Why is that

1. I have a bunch of Nanopore long-read fastq files that I need to assembly using stringtie. I converted them to bam files using minimap2 and samtools: here is what...

rattle correction step giving error

9

I ran rattle correct on my input files through snakemake. I get an error message saying this: Error in rule cluster_correction: jobid: 13 input: data/.../.../samplefile.fastq output: data/RATTLE_out/samplefile/corrected.fq, data/RATTLE_out/samplefile/uncorrected.fq, data/RATTLE_out/samplefile/consensi.fq log:...