124629
73473
59383
59045
219
58826
33
58793
0
58793
35
35
25842
32916
287
Pipeline results dir: ../lncRNA_pipeline-tri/
Filter short transcripts:
	> grep '>' ../lncRNA_pipeline-tri//step_1-filter_short/long_transcripts.fasta | wc -l
transcripts remaining

Filter long orfs:
	> grep '>' ../lncRNA_pipeline-tri//step_3-filter_long_b/no_orfs.fasta | wc -l
sequences remaining

Filter known proteins:
	> grep '>' ../lncRNA_pipeline-tri//step_5-read_nr_results/no_known_protein.fasta | wc -l
sequences remaining

Use CPAT to filter potential coding transcripts
	> grep '>' ../lncRNA_pipeline-tri//step_6-run_cpat/non_coding.fasta | wc -l
 non coding transcripts remaining
Identify using RNA Central:
	> grep '>' ../lncRNA_pipeline-tri//step_7-blastn_rna_central/non_coding.to.rnacentral_species_specific_ids_found.fasta | wc -l
found
	> grep '>' ../lncRNA_pipeline-tri//step_7-blastn_rna_central/unknown_ncRNA.fasta | wc -l
unknown transcripts remaining

Identify circRNA:
	> grep '>' ../lncRNA_pipeline-tri//step_8-circRNA/unknown_ncRNA.to.circ_base_found.fasta | wc -l
found
	> grep '>' ../lncRNA_pipeline-tri//step_8-circRNA/unknown_ncRNA.to.circ_base_missing.fasta | wc -l
unknown transcripts remaining

Identify piRNA:
	> grep '>' ../lncRNA_pipeline-tri//step_9-piRNA/unknown_ncRNA.to.all_found.fasta | wc -l
found
	> grep '>' ../lncRNA_pipeline-tri//step_9-piRNA/remaining.fasta | wc -l
unknown transcripts remaining

Identify using Infernal (RFAM):
	> grep '>' ../lncRNA_pipeline-tri//step_11-analyze_infernal/not_lnc-rfam.fasta | wc -l
found
	> grep '>' ../lncRNA_pipeline-tri//step_11-analyze_infernal/not_lnc-rfam.fasta | wc -l
unknown transcripts remaining

Identify possible lncRNA, using lncRNAnet:
	> grep '>' ../lncRNA_pipeline-tri//step_13-analyze_lncRNAnet/lncRNA.fasta | wc -l
found
	> grep '>' ../lncRNA_pipeline-tri//step_13-analyze_lncRNAnet/others.fasta | wc -l
unknown transcripts remaining

Combining all known RNA identified:
	> grep '>' ../lncRNA_pipeline-tri//step_14-concat_found/found_rna.fasta | wc -l
transcripts