Hi,

I am trying to use RepeatMasker to create a GTF file of transposable elements (specifically LTRs) from S.pombe (none already available). My aim is to load this GTF file onto IVG browser to compare LTR locations with ChiPseq data and RNAseq data.

I have downloaded the necessary files to run repeatmasker but there seems to be an issue with the configuration step.

Upon entering the RepeatMasker directory:

perl ./configure

TRF PROGRAM

This is the full path to the TRF program. This is now used by RepeatMasker to mask simple repeats.

Enter path [ /Volumes/T7_Touch/r_mask/trf409.macosx ]: Add a Search Engine:

1. Crossmatch - Phrap [ Configured ]

   1. RMBlast - Improved NCBI Blast [ Configured, Default ]

   2. HMMER3.1 & DFAM [ Un-configured ]

   3. ABBlast/WUBlast [ Un-configured ]

   4. Done

Enter Selection: 5 -- Setting perl interpreter...

Congratulations! RepeatMasker is now ready to use.

The program is installed with a the following repeat libraries:

Dfam database version Dfam_3.1

RepeatMasker Combined Database: Dfam_3.0

Further documentation on the program may be found here:

/Volumes/T7_Touch/r_mask/RepeatMasker/repeatmasker.help

So then I enter the help file:

(base) MACMB80305:RepeatMasker u1984277$ /Volumes/T7_Touch/r_mask/RepeatMasker/repeatmasker.help

/Volumes/T7_Touch/r_mask/RepeatMasker/repeatmasker.help: line 2: RepeatMasker: command not found

/Volumes/T7_Touch/r_mask/RepeatMasker/repeatmasker.help: line 3: Developed: command not found

/Volumes/T7_Touch/r_mask/RepeatMasker/repeatmasker.help: line 4: Please: command not found /Volumes/T7_Touch/r_mask/RepeatMasker/repeatmasker.help: line 4: Green,: command not found /Volumes/T7_Touch/r_mask/RepeatMasker/repeatmasker.help: line 5: http://www.repeatmasker.org: No such file or directory /Volumes/T7_Touch/r_mask/RepeatMasker/repeatmasker.help: line 7: The: command not found /Volumes/T7_Touch/r_mask/RepeatMasker/repeatmasker.help: line 8: syntax error near unexpected token (' /Volumes/T7_Touch/r_mask/RepeatMasker/repeatmasker.help: line 8:those found in "RepBase Update (http://www.girinst.org/)'

(base) MACMB80305:RepeatMasker u1984277$ ./RepeatMasker -help

-bash: ./RepeatMasker: perl: bad interpreter: No such file or directory

I'm not sure how to go about this problem, I checked the perl files and they're unix compatible

I am using Mojave 10.14.6 macOS

Or if anyone knows another way to visualise LTRs on IGV for direct visual comparison against Bam/tdf files that would help too.

Any help would be greatly appreciated,

Hannah