SpliceMap 3.3 Released - Improved long-read sensitivity

[hjanime]

Hi
Glad to hear that new useful feature has been added,
But I have one runtime problem below:

################################
genome/chr1.fa
--== SpliceMap 3.3 Junction Discoverer ==--
Developed by Kin Fai Au and John C. Mu

http://www.stanford.edu/group/wonglab/SpliceMap/

____________

Loading configuration file... run.cfg
Reading read-file-list files!...
Sequencer full read length: 75
List 1:
temp/read_1_1
List 2:
temp/read_1_2
____________
Reading and indexing reference genome!...
Chromosone name: chr1
Chromosone Size: 247249719
Index creation time: 72.4036 s.
Index sorting time: 2.02698 s.
____________
Reading and finding search seeds!...
in ... read_1_1.1-50.seq
terminate called after throwing an instance of 'std:ut_of_range'
what(): basic_string::substr
find: `./bin/SpliceMap' terminated by signal 6
genome/chr8.fa

could be the reason and how do I fix it ?
My OS is Ubuntu 10.4 AMD64
I am not sure if this applies to all other linux kernel versions.

Thanks very much.

[lix]

OK, thank you so much.

[john_mu]

Hi Lix,

Thanks for your interest, I'll try my best to help you.

However, firstly could you please email me your run.cfg file and a log of your SpliceMap run? johnmu (at) stanford.edu

I'll respond to you via email and then post here, when we have solved the problem.

Sorry, that it did not work straight away.

John Mu

[lix]

Hi,
Thanks for this good tool. It's very fast and easy to use. But it seems that I did something wrong when I used it.
I followed the tutorial as the website describes and edited the run.cfg file when running my own data. The problem may lie in the genome.
I choosed "bowtie" as the mapping way, so I downloaded the index reference from the bowtie website like h_sapiens.1.ebwt, h_sapiens.2.ebwt, h_sapiens.3.ebwt, h_sapiens.4.ebwt, h_sapiens.rev.1.ebwt, h_sapiens.rev.2.ebwt, and also, downloaded the hg18 chromosome files(chromFa.fa) like chr1.fa, chr2.fa,.... After that, I simply put all these files into the same directory like "genome" while not putting all the FASTA chromosome files into a same file, such as the CMD "cat chr*.fa > hg18.fa", as it didn't work.
After running, the output file didn't show any mapped results, only the information like "
@HD VN:1.0 SO:coordinate
@SQ SN:chr1 LN:247249719
@SQ SN:chr10 LN:135374737
@SQ SN:chr11 LN:134452384
@SQ SN:chr12 LN:132349534
@SQ SN:chr13 LN:114142980
@SQ SN:chr14 LN:106368585
@SQ SN:chr15 LN:100338915
@SQ SN:chr16 LN:88827254
@SQ SN:chr17 LN:78774742
@SQ SN:chr18 LN:76117153
@SQ SN:chr19 LN:63811651
@SQ SN:chr2 LN:242951149
@SQ SN:chr20 LN:62435964
@SQ SN:chr21 LN:46944323
@SQ SN:chr22 LN:49691432
@SQ SN:chr3 LN:199501827
@SQ SN:chr4 LN:191273063
@SQ SN:chr5 LN:180857866
@SQ SN:chr6 LN:170899992
@SQ SN:chr7 LN:158821424
@SQ SN:chr8 LN:146274826
@SQ SN:chr9 LN:140273252
@SQ SN:chrX LN:154913754
@SQ SN:chrY LN:57772954
@PG ID:SpliceMap VN:3.3
"
I've tried using the reads to align a certain chromosome such as the chr21, and it worked well as expected, but it failed when using the genome as I described above.

I'm sorry for my clumsy understanding. Any kind suggestion is appreciated.


lix

[john_mu]

Hi Everybody,

SpliceMap 3.3 has just been released. The main change is significant improvements to sensitivity when aligning long RNA-seq reads. The following 3.3.x releases will focus on usability.

New Website: http://www.stanford.edu/group/wongla...Map/index.html

Please check the website for descriptions of the new features.

Please let me know if there are any concerns.