How to run Transeq?
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Entering edit mode
7 months ago

Hello, I would like to use Transposeq for the analysis of transposition in human sequences. I ran the following command:

RUN_TRANSPOSEQ.sh NORdedup.bam TUMdedup.bam N-samp T-samp "19" containingFolder containingFolder 27 90 5 fasta fastafile queue &

where:

RUN_TRANSPOSEQ.sh = exe file for Linux machines provided by Transeq
NORdedup.bam TUMdedup.bam = control and case deduplicated bam files
N-samp T-samp = given name to these samples 
"19" = genome reference; I used GRCh38, thus 19...
containingFolder = working directory for subfolders and files
27 = min alignment parameter
90 = min % identity
5 = min read necessary to support candidate event
fasta = name of retrotransposons database [which I don't know]
fastafile = path to fast
queue = LSF queue to send jobs to [which I don't know]

I downloaded a set of reference files from the website, which contains two human genome folders (hg18 and hg19) plus a series of bed files. The manual is not there and I receive no answer from the maintainer.

When I run, I get:

$ Tumorbam is ~/NORdedup.bam
Normalbam is ~/TUMdedup.bam
Tumor type is  N-samp
Sample is  T-samp
Hgnum is 19
Directory is ~/containingFolder
Reads folder is ~/containingFolder
Evalue is 27
nalign is 90
percent identiy is 5
nreads is fasta
fasta name is fastafile
fastafile is queue
queue is

And then it stuck there. Would you know how to run Transeq?

software error use sequencing • 256 views
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Entering edit mode

Retrotransposon database files seem to be on the page (in that table) you linked for the software.

queue is from the LSF job-scheduler. If you don't have a job scheduler then you will need to omit that option. Assuming this software does not require a cluster to run.

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Entering edit mode

OK, so I can omit the last parameter. But what are fasta and fastafile? In the example it is said "L1s" and /home/L1s.fasta but these files are not in the folder associated with Transeq...

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