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Hi,
The data I have are RNA data, more precisely from the TruSeq stranded Illumina.
They were processed in the pipeline snakemake I developed with a first FASTQC, a trimming with cutadapt to eli…
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Hi OPERA-MS makers,
I have tried thet tool using the command
```
(base) pengxi@ubuntu_r740:~/softwares/OPERA-MS$ perl OPERA-MS.pl --contig-file /home/wangdanrui/HLa/metaspades/HLa_contigs.fasta -…
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```
Hi,
I'm trying to figure out how to run a second mapping pass, as described in the
paper
"It is also possible to run a second mapping pass, supplying it with splice
junction loci found in the …
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### Initial checklist
- [X] I read the [support docs](https://mdxjs.com/community/support/)
- [X] I read the [contributing guide](https://mdxjs.com/community/contribute/)
- [X] I agree to follow …
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Hello,
I'm having an issue running this pipeline with a new genome index. This install works very well when aligning to human, but with a STAR index/genome/GTF file for another species it fails afte…
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We want to use lotus2 to analyze ITS sequences. A common issue is the read-through into the opposite primer as described in the dada2 toturial: https://benjjneb.github.io/dada2/ITS_workflow.html
Can …
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### Source Name
BioStudies ArrayExpress
### Source URL
https://www.ebi.ac.uk/biostudies/arrayexpress
### Source Description
The functional genomics data collection (ArrayExpress), stores data fro…
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Hi Alex,
We are developing a workflow that involves mapping sets of short nc RNA reads to the miRBase (mature micro RNAs) database. We would like to use STAR for this alignment. We have adjusted the …
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Should short reads from metagenomic data be mapped to those genes (or protein) (>90% identity for blastx or diamond blastx for example) that were found in the database to calculate relative abundance…
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**Project:**
I would like to make an open-source, readily available automated pipeline to close bacterial genomes with long read technologies and then fixing errors by mapping short reads to them. Fo…