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cds
cd my_rnaseq_course
#If you've already copied day_3 stuff over, ignore next line
cp -r /corral-repl/utexas/BioITeam/rnaseq_course_2015/day_3/cufflinks_results .
cd day_3/cufflinks_results |
Step 1: Tophat
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#If you have a local copy:
ls -l C1_R1_clout
#If you don't have a local copy:
ls -l /corral-repl/utexas/BioITeam/rnaseq_course_2015/day_3/cufflinks_results/C1_R1_clout
-rw------- 1 daras G-801020 627673 May 17 16:58 genes.fpkm_tracking
-rw------- 1 daras G-801020 1021025 May 17 16:58 isoforms.fpkm_tracking
-rw------- 1 daras G-801020 0 May 17 16:50 skipped.gtf
-rw------- 1 daras G-801020 14784740 May 17 16:58 transcripts.gtf
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DESCRIPTION OF TRANSCRIPTS.GTF FILE
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The secret lies in the gene_id column. #For counting novel entries grep 'CUFF' C1_R1_clout/transcripts.gtf |wc -l 5484754936 #For counting entries corresponding to annotated genes grep -v 'CUFF' C1_R1_clout/transcripts.gtf |wc -l 8864488724 What do you think grep -v does? |
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| Priority | Code | Description | |
| 1 | = | Complete match of intron chain | |
| 2 | c | Contained | |
| 3 | j | Potentially novel isoform (fragment): at least one splice junction is shared with a reference transcript | |
| 4 | e | Single exon transfrag overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment. | |
| 5 | i | A transfrag falling entirely within a reference intron | |
| 6 | o | Generic exonic overlap with a reference transcript | |
| 7 | p | Possible polymerase run-on fragment (within 2Kbases of a reference transcript) | |
| 8 | r | Repeat. Currently determined by looking at the soft-masked reference sequence and applied to transcripts where at least 50% of the bases are lower case | |
| 9 | u | Unknown, intergenic transcript | |
| 10 | x | Exonic overlap with reference on the opposite strand | |
| 11 | s | An intron of the transfrag overlaps a reference intron on the opposite strand (likely due to read mapping errors) |
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