NGS-Graph-Generator2

Pre-requisites

Required tools:

• Python (version 2.7)
• Samtools (version 1.4)
• Sambamba (version 0.6.6)
• BEDTools (version 2.25.0)
• Blast+ (version 2.6.0)

Please install/add the above tools prior to running this pipeline. The tool versions used in the developing this pipeline are indicated in the bracket. Please modify line 2 to 9 in generate_network.sh to the paths/commands for these tools on your system. Once the modifications are done, run generate_network.sh to create alternative-splicing network graphs.

Input options

Required:

• b : Folder with BAM files
• g : GTF file (matching the genome build for bam alignment)
• n : A text file with gene names in each line

Optional:

• o : The output folder (default “output”)
• c : The cache directory (default “cache”)
• p : The percentage similarity value (default 85)
• l : The percentage coverage value (default 30)
• u : The method used to unify reads. Options are: by_seq (by 100% sequence identity), by_coord (by same start and end positions) (default), no_blast (by binning the chromosome positions into specific intervals, require the -r setting)
• a : If sample annotation is supplied, node/edge are averaged within specified groups
• s : Folder with sorted input bam files.

Example 1:

bash generate_network.sh
-b input_bam
-n gene_list.txt
-g input_gtf/Mus_musculus.GRCm38.91.chr.gtf

Example 2:

bash generate_network.sh
-b input_bam
-n gene_list.txt
-g input_gtf/Mus_musculus.GRCm38.91.chr.gtf
-a sample_annotation.txt
-o output
-u no_blast
-s input_bam