theheking

I am currently using tensorflow==2.2 and keras==2.4.3 with Janggu in conda environment supplied below. My environment runs smoothly until I apply a Bidirectional LSTM keras layer. This outputs a an...

MetaSpades Error code 11

1

I have run MetaSpades with all 99 other samples. With this sample it has finished abnormally with err code: -11. I have already rerun it 3 different times. Please advise,...

Err Code :-11

1

== Error == system call for: "['/sw/bioinfo/spades/3.13.1/rackham/bin/spades-core', '/domus/K55/configs/config.info', '/domus/K55/configs/mda_mode.info', '/domus/K55/configs/meta_mode.info']" finished abnormally, err code: -11 I've attached the params.txt and spades.log files as well. Any idea what might be causing...

I have great success running Spades on 370/390 of my files, however it is failing on the remaining 20. One of the recurring issues is err code 9. I was...

Assessing Read Quality: Improve the visualisation of Phred Quality Scores

1

I think the Details on the FASTQ format section is fairly confusing for beginners. For a better readibility and understanding of the quality scores. I think that the sentence "This...

Rhapsody addition?

3

Hi, I would love to be able to utilise kallisto bustools to BD Rhapsody single cell analysis however, it is not included in `kb --list` for technologies. Is there a...

Only outputting one file?

5

Hi, I am running polyester using the following code: `simulate_experiment(EnsemblfastaFile, numreps=c(1,1),fold_changes=fold_changes, reads_per_transcript=readspertx, paired=FALSE, outdir="/mnt/lustre/users/k1632479/polyester/simulatedread", distr="empirical", error_model="illumina5", bias="rnaf") ` It runs for hours and outputs a large 8 GB fasta file....