-
Hi!
I recently prepared PIPseq (v4) libraries from lentivirus-transfected cells. This includes running the fastq files through pipseeker package for read mapping, where I can get out possorted bam f…
-
Hi,
I'm trying to use dada2 to analyse PacBio 16S full amplicon data. I only have four samples which I filtered with these settings:
```
> track2 print(track2)
re…
-
Hi!I'm the beginner there!when I run the example code `cycads --fastq /opt/Cycads/test/ecoli.fq.gz --output_dir /data/work --sample_name fa `,there generate folder fa.so after quality control,whic…
-
When ran doctor.py I got fastq-dump error, below.
doctor.py
# Doctor! Doctor! Give me the news.
# Checking symptoms ...
# bwa ... OK
# datamash ... OK
# fastqc -h ... OK
# …
-
Hello,
We are currently running our _de novo_ transcriptome assembly project. We ran isONclust and isONcorrect separately instead of `isON_pipeline.sh` pipeline. Everything was perfectly fine until t…
-
Hi devlopers of Dorado,
First, thank you for providing this great software.
I noticed that after issue #532 , `RG` tag and some other tag is automatically added to the FASTQ header, which I …
-
With FastQC v0.12.1 (bioconda hdfd78af_0) on RHEL 9.4, we're seeing a discrepancy when using the "-d" and "--dir" flags to specify a non-standard directory for temporary files
```
$ fastqc -d "/te…
-
### Description of the bug
Hello, I am very grateful for your development of the Sarek pipeline. This pipeline has been very helpful to me in handling WGS analysis. However, I encountered an error wh…
-
Hi,
Hope you are having a good summer.
```
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS
ORFik 1.24.0
```
I tried to see what is causing …
-
Hello, I was attempting the following codes as you described to filter out host sequences:.
"host sequences:
mkdir host not_host
samtools fastq -F 3588 -f 65 output.bam | gzip -c > host/output_S_…