Identify Camel_TRF

[atalgarni]

Identify Arabian camel tandem repeats

1. Identify Tandem repeat using TRF tool found at https://tandem.bu.edu/trf/trf.download.html

• Run the TRF using default setting: trf409.macosx (input genome.fasta) 2 7 7 80 10 50 2000 -d -f -m or use -h instead of -d

2. Clean up the output of TRF tool using perl script found at http://archive.gramene.org/db/markers/ssrtool or simply copy the following link to download the source code and run it as perl ssr.pl input file(TRF.dat file) > output ftp://ftp.gramene.org/pub/gramene/archives/software/scripts/ssr.pl

the files will be added shortly!!!!!

[atalgarni]

Please Manee could you add Mohand; his user name is bioinfo24091...... thanks

[atalgarni]

You can now visualize the Camel TRF on https://www.ncbi.nlm.nih.gov/genome/gdv/browser/?context=genome&acc=GCF_000767585.1 from the checklist on the lift chose Your data and then upload the camel trf track file found at https://github.com/kacst-bioinfo-lab/labwork/blob/master/doc/shared/Camel_TRF_Track.bed.zip

[MManee]

• we used perf tool to identify SSR motifs
• the tool seems to work well to identify perfect SSRs PERF GitHub Page