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Targeted Iso Seq QC Wiki
Magdoll edited this page Aug 15, 2017
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Last Updated: 08/15/2017
This wiki shows scripts used for targeted Iso-Seq analysis.
- BioPython
- bx-python
You can install BioPython via pip install biopython
and bx-python via pip install bx-python
. It is highly recommended that you do such installations in a virtual environment via Anaconda or python's own virtualenv to have a clean environment to work with.
No installation is required. You just download the Cupcake repository from GitHub and add the appropriate paths.
$ git clone https://github.com/Magdoll/cDNA_Cupcake.git
$ export PYTHONPATH=$PYTHONPATH:<path_to>/cDNA_Cupcake/sequence
To see that you have successfully gotten BioPython, bx-python, and the sequence/
subdir working, try the following in Python interpreter:
$ python
Python 2.7.13 |Anaconda 2.4.1 (64-bit)| (default, Dec 20 2016, 23:09:15)
>>> import Bio # testing BioPython
>>> import bx # testing bx-python
>>> import BED # testing Cupcake sequence/
All of the above should work without error messages.
You will need:
- The input fasta file
- The aligned SAM file (see GMAP command below)
- A tab-delimited probe BED file with at least the first three columns and an optional 4th column of
<chrom> <start> <end> <gene_name>
. No headers allowed!
You can generate the aligned SAM file using GMAP:
gmap -D ~/share/gmap_db_new/ -d hg19 -f samse -n 0 -t 30 -z sense_force \
isoseq_flnc.fasta \
> isoseq_flnc.fasta.hg19.sam \
2> isoseq_flnc.fasta.hg19.sam.log