Awesome
TelSeq is a software that estimates telomere length from whole genome sequencing data (BAMs).
The most current development version is available from our git repository: git://github.com/zd1/telseq.git
The software is implemented in C++.
Citation:
Estimating telomere length from whole genome sequence data
Zhihao Ding; Massimo Mangino; Abraham Aviv; Tim Spector; Richard Durbin. Nucleic Acids Research 2014; doi: 10.1093/nar/gku181 http://nar.oxfordjournals.org/content/42/9/e75
Compile TelSeq
TelSeq dependency:
-
the bamtools library (https://github.com/pezmaster31/bamtools)
-
A modern version of GCC (version 4.8 or above) This can been seen by "gcc --version". If multiple GCCs are installed in your system, please set environmental variables pointing to the one of version 4.8 or above. e.g. in bash,
export CXX=/path/to/gcc/gcc-4.8.1/bin/g++
export CC=/path/to/gcc/gcc-4.8.1/bin/gcc
One easy way to install a new GCC is to use homebrew,
# install homebrew if you don't have it
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
# install GCC
brew install gcc
Compile
Go to the src directory and run autogen.sh from the src directory to generate the configure file
./autogen.sh
Then run
./configure
make
The executable binary will be at src/Telseq/telseq. If bamtools are installed not at the system location, you can specify their location by
./configure --with-bamtools=/path/to/bamtools
The /path/to/bamtools directory is the directory that contains 'lib' and 'include' sub directories.
Run TelSeq
Read options and usage information
telseq
Analyse one or more BAMs by specifying BAM file path as command line arguments.
telseq a.bam b.bam
Analyse a list of BAMs whose paths are specified in a 'bamlist' file.
bamlist should contain only 1 column with each row the path of a BAM. i.e.
/path/to/a.bam
/path/to/b.bam
telseq -f bamlist
BAM file path can also be provided by piping in a 'bamlist', whose format must be same as above
cat bamlist | telseq
output
By default the result will be printed out to stdout. To change it to a file, use '-o' option to specify a file path. i.e.
telseq -o /path/to/output a.bam b.bam c.bam
This can also be achived by just direct the output to a file using '>', i.e.
telseq a.bam b.bam c.bam > /path/to/output
The software will print out running status to stderr as well. To separate them from stdout, one could direct log to a file, ie.
telseq a.bam b.bam c.bam 2>outputlog
Merge results from read groups by taking a weighted mean. However, it is benetifical run without
-m to output the result per lane, so to have an idea about inter-lane variation. The merging
can be done afterwards.
telseq -m a.bam > output
Output file format
| Column | Definitions |
|---|---|
| ReadGroup | read group, Defined by the RG tag in BAM header. |
| Library | sequencing library that the read group belongs to. |
| Sample | defined by the SM tag in BAM header. |
| Total | total number of reads in this read group. |
| Mapped | total number of mapped reads, SAM flag 0x4. |
| Duplicates | total number of duplicate reads, SAM flag 0x400. |
| LENGH_ESTIMATE | estimated telomere length. |
| TEL0 | read counts for reads containing no TTAGGG/CCCTAA repeats. |
| TEL1 | read counts for reads containing only 1 TTAGGG/CCCTAA repeats. |
| TELn | read counts for reads containing only n TTAGGG/CCCTAA repeats. |
| TEL16 | read counts for reads containing 16 TTAGGG/CCCTAA repeats. |
| GC0 | read counts for reads with GC between 40%-42%. |
| GC1 | read counts for reads with GC between 42%-44%. |
| GCn | read counts for reads with GC between (40%+n*2%)-(42%+(n+1)*2%). |
| GC9 | read counts for reads with GC between 58%-60%. |
By default for each BAM a header line will be printed out. This can be suppressed by using the '-H' option. It is useful when one has multiple BAMs to scan and wish the output to be merged together. i.e.
telseq -H a.bam b.bam c.bam > myresult
To just print out the header, use '-h' option. i.e.
telseq -h
Docker
Install Docker
Please refer to the official website for installing Docker https://docs.docker.com/engine/installation/
Build telseq Docker image
docker build -t telseq-docker github.com/zd1/telseq
Run telseq
Note that the sample path "/path/to/bam/sample.bam" in the machine that the container is run needs to be specified. "/sample.bam" doesn't need to be changed.
docker run -v /path/to/bam/sample.bam:/sample.bam telseq-docker /sample.bam
Contact
zhihao.ding at gmail.com