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repeatmasker plain text into gtf

THIS IS MY PLAIN TEXT FILE:

 cat filtered_for_repeatsgtf.txt |head

239 chr1    67108752    67108881    +   RLTR17B_Mm  LTR ERVK
314 chr1    3145673 3145796 -   RMER16A3    LTR ERVK
3620    chr1    5242237 5242959 -   RMER13B LTR ERVK
1530    chr1    7339880 7340133 -   MYSERV6-int LTR ERVK
2842    chr1    9436682 9437312 +   RLTR1D2_MM  LTR ERV1
1317    chr1    28311234    28311561    -   MTD LTR ERVL-MaLR
4789    chr1    29359731    29360380    -   MERVL_2A-int    LTR ERVL
2845    chr1    34602700    34603167    -   RLTR10  LTR ERVK
4419    chr1    45088448    45089377    -   RLTR13D6    LTR ERVK
287 chr1    60817355    60817487    +   LTR33   LTR ERVL

I want to convert this into ensebml gtf format: i.e

 cat Mus_musculus.GRCm38.99.withchr.gtf|head 
chr1    havana  gene    3073253 3074322 .   +   .   gene_id ENSMUSG00000102693; gene_version 1; gene_name 4933401J01Rik; gene_source havana; gene_biotype TEC;
chr1    havana  transcript  3073253 3074322 .   +   .   gene_id ENSMUSG00000102693; gene_version 1; transcript_id ENSMUST00000193812; transcript_version 1; gene_name 4933401J01Rik; gene_source havana; gene_biotype TEC; transcript_name 4933401J01Rik-201; transcript_source havana; transcript_biotype TEC; tag basic; transcript_support_level NA;

is there any tool or script to do this?

sequencing next-gen alignment
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updated by Dave Carlson Dave Carlson • written by priya120195 • priya120195

1 answer

Note that RepeatMasker comes with a utility script to convert their default *.out file format to GFF3. You can find it at:

/path/to/RepeatMasker/util/rmOutToGFF3.pl

If you specifically need GTF format, you can convert using awk as Pierre suggested or using an existing tool (e.g., see here).

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written by Dave Carlson Dave Carlson

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