genetype
The commands under this group takes a gene annotation file in gff format and an alignment file in bam format as inputs, computes and plots the distribution of read lengths over different gene types (protein coding, lncRNA, snoRNA etc) as interactive line plots.
parse-gene-type-read-length
Given a gene annotation file in gff format and an alignment file in bam format, compute the distribution of read lengths over different gene types (protein coding, lncRNA, snoRNA etc), and write the output in json format.
Options
option |
description |
required |
default value |
|---|---|---|---|
–gff3 |
Gene annotation file in gff format (supports .gz files) |
✓ |
|
–bam |
Alignment file in bam format (MUST be co-ordinate sorted and indexed) |
✓ |
|
–out-json |
Output file to write json formatted data |
✓ |
|
–gene-features |
Features to parse from GFF3 file, MUST be supplied as: |
✗ |
|
–gene-id |
Gene id attribute in GFF3 attribute column |
✗ |
gene_id |
–gene-type |
Gene type attribute in GFF3 attribute column |
✗ |
gene_type |
–min-q |
Minimum alignment quality |
✗ |
0 |
–ignore-duplicate |
Flag to ignore PCR duplicate reads (after samtools markdup) |
Usage
ngs-statter parse-gene-type-read-length --gff3 path/to/annotation.gff3.gz --bam path/to/alignment.bam --out-json path/to/output.json
plot-gene-type-read-length
Given a list of json files containing read length distribution over gene types (generated using parse-gene-type-read-length), plot the read length distribution as an interactive (html) line plot.
Options
option |
description |
required |
default value |
|---|---|---|---|
–json-dir |
Directory containing json formatted read length per gene type files (see parse-gene-type-read-length). Either –json-dir or json formatted files as space separated arguments MUST be provided |
✗ |
|
–html |
Output file name |
✓ |
|
–pattern |
If –json-dir is provided, use this pattern to match files |
✗ |
*.json |
Usage
using --json-dir
# using --json-dir
ngs-statter plot-gene-type-read-length --json-dir path/to/json_dir --html path/to/output.html
using space separated json files as arguments
# using space separated json files as arguments
ngs-statter plot-gene-type-read-length --html path/to/output.html path/to/bam1.json path/to/bam2.json