SpliceMap

Getting Started

These simple steps will help you integrate SpliceMap into your transcriptomics analysis pipeline.

Read the requirements for running SpliceMap.
Download and set-up the SpliceMap package
Follow the tutorial to see how SpliceMap works on some example data.
Check the manual if anything is unclear.
You're ready, Happy SpliceMapping!

Publication

Kin Fai Au, Hui Jiang, Lan Lin, Yi Xing, and Wing Hung Wong
Detection of splice junctions from paired-end RNA-seq data by SpliceMap
Nucleic Acids Research, Advance access published on April 5, 2010. [preprint]

Latest News

10-23-2010: SpliceMap 3.3.5.2 Released

This release fixes a bug regarding multi-hits.

(another) Multi-hit bug fix

10-1-2010: SpliceMap 3.3.5.1 Released

This release fixes a bug regarding multi-hits and has some new features.

Multi-hit bug fix
New option "max_multi_hit" specifies the maximum number of multi-hits allowed in the seeding (not the full reads).
Small formatting issue in SAM/coveraege file fixed

9-20-2010: SpliceMap 3.3.5 Released

This release has a large part re-implemented for increased reliability and speed. There are also new options to improve the alignment. Future versions will focus on improving the alignment sensitivity by rescuing some pair reads. In the next point release we will try to associate junctions with an annotated gene name.

Able to set the number of maximum number of mismatches in each read
SAM output shows the number of mismatches in each read
SAM output shows where the mismatches lie
SAM output shows the number of soft clipped bases in each read
Able to set the number of maximum number of bases clipped in each read
SAM output shows the number multiple hits of each read
SAM output indicates the inferred insert size
SAM output correctly indicates if a pair is not mapped
Memory usage much less dependent on total number of reads
Non-unique coverage outputted by default, this is no longer an option and requires no extra memory
Includes latest version of Bowtie (0.12.7)

9-5-2010: SpliceMap 3.3.3.2 Released

This release reduces the memory requirement significantly for large datasets, improves stability and introduces some new features. The next version will further reduce memory consumption.

Support for almost unlimited number of chromosomes and read files
Able to read concatenated genome files (you and even mix and match multiple FASTA reference files)
Checks bowtie index to make sure it is valid
Able to map 'bad' reads with residual adaptor sequences
Stability improvements
Reduced memory consumption

8-23-2010: Memory usage issue

Note that SpliceMap 3.3.3.1 uses over 50GB for 200 million reads. In the next version we will reduce this requirement significantly.

8-19-2010: SpliceMap 3.3.3.1 Released

This release fixed a bug in the SAM file output of quality scores.

8-18-2010: SpliceMap 3.3.3 Released

SpliceMap 3.3.3 bring a number of new features. Most notable is the support for uneven read lengths in both pairs. For example, if reads in your pairs range from [50-73bp] due to trimming, SpliceMap will happily align them. Upcoming features in future releases include a "NM" tag for each read in the SAM file, support for concatenated genome files and options for extra specificity from long reads. The changes in 3.3.3 are listed below:

Support for trimmed reads with uneven length
Option to run multiple chromosomes are the same time (at the cost of memory) [num_chromosome_together]
Read quality is now copied to the SAM file
Read names are copied to the SAM file
Option to change the location of "temp" and "output" folders
Non-unique hits are marked with MAPQ = 0 in the SAM file
Faster alignment by ignoring redundant reads
Bowtie index is automatically built, if it is not found
SAM file sorted properly for cufflinks
Less verbose, output logs redirected to "debug_logs" folder
More checking of reads/genome

7-6-2010: SpliceMap 3.3.1.3 Released -- Single-read bug fixed

SpliceMap 3.3.1.3 fixes the single-read bug. Now, you may use single-read data just like pair-reads. The next update of SpliceMap will be quite significant (so may take a while).

Also fixed a bug with the display of "max_intron" and "min_intron"

7-2-2010: Single-read bug

There has been a bug discovered regarding the use of single-reads. When the new code was added for improved long pair-reads, it was not updated for single-reads by me (John Mu). Very sorry about that! There have been a number of problems as a result of this for people who use single-reads, including not discovering many junctions.

A fixed version will be out in a few days, with an announcement.

Please note: If you use pair-reads, there is nothing to be worried about. It is fine.

6-30-2010: SpliceMap 3.3.1.2 Released

SpliceMap 3.3.1.2 fixes some bugs and adresses compatibility issues. If you have an older system and had problems running previous version of SpliceMap, this version might help. SAMtools now works properly with the SAM output.

Removed trailing tab from the SAM output. If you have existing SAM files and do not want to re-run SpliceMap, simply strip off the last tab character and the file will work with SAMtools.
Addressed a file handling issue with older versions of g++
Binaries are now compiled by default by an older version of g++ for maximum compatibility. If you have a newer version of linux, I suggest you recompile the binaries with "install.sh" and "install-bowtie.sh" for maximum performance.

6-17-2010: SpliceMap 3.3.1 Released

SpliceMap 3.3.1 is a bug fix release. There were some problems with the new wild-card expression for chromosome files so we have reverted to the old one and added an option in the .cfg file.

Reverted to using "chr*.fa" to detect chromosome by default.
Added "chromosome_wildcard" option to the .cfg file for people with chromosome in different formats