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I'm trying to get a pipeline working with single-end reads sample as an input. The pipeline has been defined but when a single-end reads sample is added to the cart and the pipeline is selected, the p…
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Hello.
I'm currently working with maftools to visualize IonTorrent NGS data which contains information about hotspot variants we've selected (i.e. ~1,400 variants).
The problem is whenever I t…
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Dear developers,
Is there a way to pass the spades flag "--iontorrent" to your pipeline or are only illumina reads allowed ?
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Dear Jeff,
I was wondering if you might be interested in a script that prepares input files for paprica from single end reads (IonTorrent). I would be happy to share.
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I searched "redbiom summarize contexts". It looks like all CTX (total 79) are for 16s study, none for ITS. Can anyone make a CTX based on ITS amplicon study?
Thanks,
Gary
ContextName Sa…
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Hi,
This is more of a fyi than an issue... :)
In order to build on a fresh cents 6.5, I had to wrap each call to `${LSB_RELEASE_CODENAME}` in quotes. Doing so made it build.
```
wget http://downl…
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Hello,
I installed LDC ldc2-1.21.0-linux-x86_64.tar.xz (also tried with ldc2-1.18.0-linux-x86_64.tar.xz),
cloned the sambamba v0.7.1 and run make.
I have got this error:
```
cd htslib && make…
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Hi developers,
I am using spades 3.14.1.
command line is:
spades.py --pe1-1 fq1 --pe1-2 fq2 -o ./spades --pe1-s fo --pe1-s re -m 20 --isolate --pe-or fr, fr
get error messages below, did't f…
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**Describe the bug**
checkdeps scripts do not check for colorid
**To Reproduce**
Steps to reproduce the behavior:
I have this bit in my dockerfile to check for all dependencies
```Dockerfile
R…
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SRR11840026 is an Ion Torrent dataset which gave a novel OTU which is most likely a false positive due to Ion sequencing.
The master assembly table has "?" for the SRR11840026 "platform" field, sa…