Thank you Mike. I will try what you suggest. Sounds like a good idea. I will let you know if it works.
Thanks,
TN
Thanks,
TN
You are currently viewing the SEQanswers forums as a guest, which limits your access. Click here to register now, and join the discussion
./build_lmer_table -l 14 -sequence yourgenome.fasta -freq ~/Desktop/Vi_14.freq
./RepeatScout -sequence yourgenome.fasta -output your_repeats.fasta -freq your_freq_table -l 14
cat your_repeats.fasta| ./filter-stage-1.prl >your_repeats_filtered1.fasta
./RepeatMasker -s -lib your_repeats_filtered1.fasta yourgenome.fasta
cat your_repeats_filtered1.fasta | ./filter-stage-2.prl --cat yourgenome.fasta.out --thresh 10 your_repeats_filtered2.fasta
./RepeatMasker -pa 4 -s -lib your_repeats_filtered2.fasta -nolow -norna -no_is -gff yourgenome.fasta
cat /group/aquaculture/mussels/sequencing/MUSSEL1/repeatscout/contigs65fullQC2.filtered.fa.gt1k.fa.repeatscout | ./filter-stage-1.prl > contigs65fullQC2.filtered.fa.gt1k.fa.repeatscout.filter1
cat /group/aquaculture/mussels/sequencing/MUSSEL1/repeatscout/contigs65fullQC2.filtered.fa.gt1k.fa.repeatscout | ./filter-stage-1.prl > contigs65fullQC2.filtered.fa.gt1k.fa.repeatscout.filter1
filter-stage-1.prl
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 08-27-2024, 04:40 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
08-27-2024, 04:40 AM
|
||
New Single-Molecule Sequencing Platform Introduces Advanced Features for High-Throughput Genomics
by seqadmin
Started by seqadmin, 08-22-2024, 05:00 AM
|
0 responses
293 views
0 likes
|
Last Post
by seqadmin
08-22-2024, 05:00 AM
|
||
Started by seqadmin, 08-21-2024, 10:49 AM
|
0 responses
135 views
0 likes
|
Last Post
by seqadmin
08-21-2024, 10:49 AM
|
||
Started by seqadmin, 08-19-2024, 05:12 AM
|
0 responses
124 views
0 likes
|
Last Post
by seqadmin
08-19-2024, 05:12 AM
|
Comment