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### Description of feature
Many labs doing ONT sequencing generate basecalled/demultiplexed FASTQ output split into multiple files in the same directory (this is in fact the default behavior of MinKN…
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Hi! I am with an issue during the read_qc step of the metaWRAP tutorial.
When I tried the command line as it is in the tutorial:
```
for F in RAW_READS/*_1.fastq; do R=${F%_*}_2.fastq; BASE=${F##…
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I am using cromwell-34.jar. I couldn't reproduce this issue with cromwell-34, 39 and 40.
This is an original input JSON.
```
{
"chip.genome_tsv": "/home/groups/cherry/encode/pipeline_genome_…
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Hello,
I'm running into "Segmentation fault (core dumped)" error when running a workflow with (or without) snakemake. I've used the same data, same tools and same parameters on several machines wit…
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A recursive find is performed for pipeline ingestion at module 4 where it is attempting to find all seq_summary files in the fastq folder following standalone CLI or MinKNOW basecall analysis. Keeping…
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I am trying to assemble RNA-seq data downloaded form SRA database and trimmed by Trimmomatic program using Trinity-v2.8.5 but get follow errors. I thought the question is the command line or file form…
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I am attempting to run Trinity 2.14.0 through Singularity. This is my code:
```
#!/bin/bash
export TRINITY_HOME=/scratch/aubfjb001/DeNovo/Trinity
FQ1="/scratch/aubfjb001/DeNovo/Trinity/C12_0_1…
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Find a way so that if genomics change the names, there is an easy way to deal with it. Either within the snakemake or a utility script to use before running the script.
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It would be great if a `in_3.fastq` could be specified. A third FASTQ file is often used for single-cell ATAC data to indicate the cell barcode. This third read, is not meant to be be mapped, but the …
ghuls updated
3 years ago
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I have 10X 3' v1 chemistry data with four fastq files:
```
EBT0_1A_S1_L001_I1_001.fastq.gz # 8 nt per read
EBT0_1A_S1_L001_R1_001.fastq.gz # 98 nt per read
EBT0_1A_S1_L001_R2_001.fastq.gz # 16 n…