-
Hi,
I am looking for some advice with Flye. I am interested in assembling different regions of a human sample. These regions are quite small and rarely exceed 20kb. Because there are quite a few of…
-
Is a way to use minimap2 seqeuence aligner for pggb pipeline?
Detailed steps will be very helpful.
Thanks.
-
Hi, thanks for the great software. I am having a problem with the `pan_genome_reference.fa` output file being incorrect during panaroo merge.
I merged two pangenome runs with the following command:…
-
**Describe the bug**
HMMRATAC's SAM reader fails:
```
Exception in thread "main" net.sf.samtools.SAMFormatException: SAM validation error: ERROR: Record 1, Read name A00836:480:HJ2W5DSXY:
2:1125…
-
Hello,
Thank you for your developing bismark for the community. We, however, observed inconsistent bismark bam output between different --multicore setting. These bams would lead to ~0.2% differenc…
-
Hi,
I am trying to run parsnp to align ~2300 bacterial genomes. However I am getting a critical error resulting in failure of Parsnp_aligner.ini. In the error log, I get a *** WARNING *** Assuming…
-
**Version info**
- bcbio version (`bcbio_nextgen.py --1.2.9a:
- OS name and version (`lsb_release -ubuntu 18.04):
**To Reproduce**
Exact bcbio command you have used:
bcbio_nextgen.py /home/user…
-
After multiple attempts of running SQANTI without having an out of memory error from our slurm cluster, I've got the following standard output:
```bash
[continue after the minimap2 log]
[M::main] R…
-
Command run on AWS EC2 instance to run docker on local instance
```bash
nextflow run /home/ubuntu/my-pipelines/nf-core/rnaseq-nfcore/rnaseq --reads '/data/dataset/SRR9667733/*_R{1,2}.fastq.gz.1' -…
-
Hi,
I'm trying to use sqanti3 to classify the transcripts sequenced from a non-model marine organism. I've clustered the pacbio reads using the isoseq3 pipeline described in the github repo of pacb…