Archived TALON Example Instructions (v4.2)

TALON example

These instructions are for TALON versions below 4.3 since the package version of TALON uses slightly different commands.

Use the provided files in TALON/example to try TALON out on chromosome 21 PacBio SAM reads from two biological replicates of human cell line GM12878.

First, initialize the TALON database from the provided GTF annotation of chromosome 21:

python ../initialize_talon_database.py \
        --f gencode.v29.chr21.gtf \
        --a gencode_v29 \
        --g hg38 \
        --o example_talon

Now, use the provided config file and the newly initialized database to annotate and quantify the reads. The database is modified in place.

python ../talon.py \
       --f config.csv \
       --db example_talon.db \
       --build hg38 \
       --o example

The file 'example_talon_QC.log' contains a record of each input transcript along with the computed coverage and identity of the alignment. During a longer TALON run, you can count the number of lines in the file in order to track how many reads have been processed so far.

Now, we can explore the results of the run. To summarize how many of each transcript type were found (prior to any filtering), run:

python ../post-TALON_tools/summarize_datasets.py \
       --db example_talon.db \
       --v \
       --o example

Notice that the number of novel transcripts is relatively high. This is because the summary script counts every transcript model in the database, regardless of whether it would pass a biological replicate reproducibility filter or not.

To create an abundance matrix without filtering (for use computing gene expression), we run the following:

python ../post-TALON_tools/create_abundance_file_from_database.py \
       --db example_talon.db \
       -a gencode_v29 \
       --build hg38 \
       --o example

We can also generate a filtered abundance matrix where we require transcripts to be either a) known, or b) detected in both replicates (for transcript-level expression):

python ../post-TALON_tools/create_abundance_file_from_database.py \
       --db example_talon.db \
       -a gencode_v29 \
       --filter \
       -p pairings.csv \
       --build hg38 \
       --o example