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 &
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?