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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 |
| Code Block |
|---|
| language | phptext |
|---|
| title | Parse gffcompare results |
|---|
| cut -f 9 results/stringtie_merged.annotated.gtf |grep 'class_code "j"'|cut -d ';' -f 3 |head| Pull out top 10 genes with potentially novel (class code j) transcripts |
|
Construct a unix command to pull out top 10 genes with potentially novel (class code j) transcripts
Hint: Use a combination of cut and grep (looking for class_code "j") |
4. Redo stringtie abundance calculations using the newly merged transcripts.
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