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Hi,
I am running MaSurCa version 3.2.6 but I got numerous Broken pipe massages which probably lead that it failed.
Here is my config file:
```
# example configuration file
# DATA is specifi…
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### Description of bug
I have paired end file from Illumina, eg. AT11B_trimmed1.fastq and AT11B_trimmed2.fastq. I have used BBMerge to merge the two files to get AT11B_merged.fastq and AT11B_unmerged…
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Hello,
I would like to know how can I change the allowed base mismatches (-m flag). I have tried these commands, but it seems not to be working:
$ ./idemp -b ../Primavera_2014/barcode_sample.txt…
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Hello there again, I am trying this pipeline again this time with fastq files and I am getting errors.
See attached txt file.
Thank you.
[error0928.txt](https://github.com/lmtani/wf-human-mito/fi…
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#Connect to remote server with -X
ssh -X {remote server}
conda install -c bioconda igv -y
conda install -c bioconda fastqc -y
#Then open a ubuntu subsystem window
igv
#Should be ableto open a n…
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Hello,
I tried to run scaff_reads on my 10X raw data with:
`scaff_data reads.dat reads_1.fastq reads_2.fastq > try.out`
Where, my reads.dat file had:
q1 = /10X_RAWDATA/S1_L008_R1_001.fastq.gz
q2=…
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I'm constructing a csv input file for a sample (from an ILLUMINA sequencer) and am a little confused about some of the fields.
Referencing [gatk](https://gatk.broadinstitute.org/hc/en-us/articles/3…
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Hi there, I am trying to use extract_kraken_reads.py to exclude the human reads.
I have kraken output file kraken.report.txt and kneaddata processed fastq file other_kneaddata.fastq as inputs:
…
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Hi ,
I want to resquiggle part of fastq records (because too many of them).
I shuffle fastq record first (to make sure sample evenly) and sample a potion from it, after running resquiggle modue…
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I am using nanopolish to call methylation. As far as I can tell `nanopolish index` indexes the entire contents of a fast5 folder and a single fastq file. So for multiple fastq file derived from the sa…