These are chat archives for cboursnell/transfuse

10th
Feb 2016
tylim
@tylim
Feb 10 2016 10:42
Hi @cboursnell , I'd like to merge 10 assemblies and had ran Transrate on each of them previously. I was wondering if there's a way where I could bypass Transrate and run Transfuse directly?
Richard Smith-Unna
@blahah
Feb 10 2016 10:57
@tylim do you mean that you want to avoid transrate being re-run by transfuse?
tylim
@tylim
Feb 10 2016 11:10
@Blahah yup
Chris Boursnell
@cboursnell
Feb 10 2016 13:16
When transfuse runs transrate it creates a directory called transrate_<fasta_file_name>. The fasta_file_name is the name without the path and the extension. For example for soap-k31.fasta it would make a directory called transrate_soap-k31. Then transrate is run. Transrate will rerun, but won't recreate the bam files and other things that take a while.
So if you put your existing transrate runs in the directory where you're running transfuse it should find them and will do a small amount of processing again (there are some extra score files that transfuse makes that transrate doesn't do normally) but it will be much faster.
├── transrate_idba
│   ├── assembly3_score_optimisation.csv
│   ├── idba
│   │   ├── Genome
│   │   ├── GenomeIndex
│   │   ├── GenomeIndexHash
│   │   └── OverflowTable
│   ├── idba.fa_bam_info.csv
│   ├── idba.fa_quant.sf
│   ├── libParams
│   │   └── flenDist.txt
│   ├── logs
│   │   ├── salmon.log
│   │   └── snap.log
│   ├── summary.txt
│   ├── yeast_1.fastq.yeast_2.fastq.idba.assigned.bam
│   ├── yeast_1.fastq.yeast_2.fastq.idba.bam
│   └── yeast_1.fastq-yeast_2.fastq-read_count.txt
├── transrate_soap
│   ├── assembly0_score_optimisation.csv
│   ├── libParams
│   │   └── flenDist.txt
│   ├── logs
│   │   ├── salmon.log
│   │   └── snap.log
│   ├── soap
│   │   ├── Genome
│   │   ├── GenomeIndex
│   │   ├── GenomeIndexHash
│   │   └── OverflowTable
│   ├── soap.fa_bam_info.csv
│   ├── soap.fa_quant.sf
│   ├── summary.txt
│   ├── yeast_1.fastq-yeast_2.fastq-read_count.txt
│   ├── yeast_1.fastq.yeast_2.fastq.soap.assigned.bam
│   └── yeast_1.fastq.yeast_2.fastq.soap.bam
this is from one of my runs of transfuse, if that helps...
tylim
@tylim
Feb 10 2016 13:20
that's wonderful, many thanks!!
Chris Boursnell
@cboursnell
Feb 10 2016 13:25
@tylim Let me know if it works ok
tylim
@tylim
Feb 10 2016 14:07
@cboursnell It worked! Thank again for your help :smiley:
Chris Boursnell
@cboursnell
Feb 10 2016 15:11
You're welcome :)