Quick Start Guide#
This page provides simple quick-start information for using Splam with BAM and GFF files. Please read the Alignment file evaluation & cleanup (BAM) or Annotation file / assembled transcripts evaluation (GFF) page for more details on each step.
If you haven't already, please follow the steps in the Installation page to install and load Splam.
Super-Quick Start (3 lines of code)#
There are two main use case scenarios of Splam. The first one is running with an alignment file and second one is running with an annotation file or assembled transcripts. Both of them can be done in three lines of code.
Before you get started, make sure you have already cloned the Splam GitHub repository. We provide a few examples below:
Example 1: clean up alignment files (BAM)#
$ cd test
# Step 1: extract splice junctions in the alignment file
$ splam extract -P SRR1352129_chr9_sub.bam -o tmp_out_alignment
# Step 2: score all the extracted splice junctions
$ splam score -G chr9_subset.fa -m ../model/splam_script.pt -o tmp_out_alignment tmp_out_alignment/junction.bed
#Step 3: output a cleaned and sorted alignment file
$ splam clean -P -o tmp_out_alignment -@ 5
Example 2: evaluate annotation files / assembled transcripts (GFF)#
$ cd test
# Step 1: extract introns in the annotation
$ splam extract refseq_40_GRCh38.p14_chr_fixed.gff -o tmp_out_annotation
# Step 2: score introns in the annotation
$ splam score -G chr9_subset.fa -m ../model/splam_script.pt -o tmp_out_annotation tmp_out_annotation/junction.bed
#Step 3: output statistics of each transcript
$ splam clean -o tmp_out_annotation -t 0.8
Splam can also run on non-human species.
Example of evaluating mouse annotation files (GFF)#
$ cd test
# Step 1: extract introns in the annotation
splam extract mouse_chr19_subset.gff -o tmp_out_generalization
# Step 2: score introns in the annotation
splam score -G mouse_chr19.fa -m ../model/splam_script.pt -o tmp_out_generalization tmp_out_generalization/junction.bed
#Step 3: output statistics of each transcript
splam clean -o tmp_out_generalization -t 0.8
Try Splam on Google Colab#
We created some reproducible and easy-to-run Splam examples on Google Colab. It's a good starting point, so go ahead and check them out!
For more detailed analysis steps, please check :
See also
