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Hello,
I'm trying to think of a way that I can use this tool to detect variants that occur more frequently in one group than another. For example, suppose I have 50 samples sequenced to 20X coverag…
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Hello,
I wanted to perform assembly on paired-end RNAseq data.
Here is the command I used:
perl ~/software/Bridger_r2014-12-01/Bridger.pl --seqType fq --left Sample1_R1_fastq.gz --right Sample…
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Subsample the input reads to the smallest input file
Or scale the results
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`seq_recovery=0.4152_0` for example, cannot be processed into a megamash table because it doesn't have any unique 16mers. This is because of a flawed assumption: ESPECIALLY in protein variant librarie…
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Hi,
After finding some relevant consecutive 31-mers, we would like to repeat the workflow with k=41 in order to focus our search. The template config.yaml discourages this, and it becomes clear fr…
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Hello, Narciso,
The tool is great! thank you again)
One question to discuss.
When I'm using filtering by default (prinseq), I have near thousand of contigs and the warning from Spades:
`Too many…
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Hi,
I am trying to run the preprocessing step of nebula on a BAM with long reads, in order to later on call it on short read BAMs. However, I am running out of memory: with the entire BED file, 450GB…
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Hello all,
I am using GATB library for my work. I have a naive question which I have not been able to find an answer for. While using one of the functions to find the abundance of a node (queryAbunda…
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Hi - saw your poster at ISMB and was hoping to try out MoSwA. Do you have a working demo example which can be run through? I tried running on my own examples but keep getting list index out of range e…