User:Lindenb/Notebook/UMR915/20101103: Difference between revisions
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Does '''polyphen''' discard the stop codon ? Testing '''polyphen''' with a stop codon: chr22:40053278 C/G should create a stop codon UA.G | Does '''polyphen''' discard the stop codon ? Testing '''polyphen''' with a stop codon: chr22:40053278 C/G should create a stop codon UA.G | ||
==Hadoop== | |||
download from http://apache.multidist.com//hadoop/core/stable/hadoop-0.20.2.tar.gz | |||
scp on server 2,3,4 | |||
==Testing GEM== | ==Testing GEM== | ||
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gem-do-index gem-fasta2loc_cont_32b gem-mappability_fm_general_64b gem-mapper_fm_general_64b gem-split-mapper_fm_general_64b | gem-do-index gem-fasta2loc_cont_32b gem-mappability_fm_general_64b gem-mapper_fm_general_64b gem-split-mapper_fm_general_64b | ||
gem-do-index_fm_dna_32b gem-fasta2loc_cont_64b gem-mappability-retriever gem-retriever</pre> | gem-do-index_fm_dna_32b gem-fasta2loc_cont_64b gem-mappability-retriever gem-retriever</pre> | ||
===Creating an index=== | |||
( http://sourceforge.net/apps/mediawiki/gemlibrary/index.php?title=Gem_do_index_man_page ) | |||
<pre>gem-do-index -i ${HG18} -o gemhg18 | |||
Welcome to GEM-do-index build 156 (beta) - (2009/10/07 02:50:12 GMT) | |||
(c) 2008-2010 Paolo Ribeca <paolo.ribeca@gmail.com> | |||
************************************************************************ | |||
* WARNING: this is a beta version, provided for testing purposes only; * | |||
* check for updates at <http://www.paoloribeca.net/software/GEM>. * | |||
************************************************************************ | |||
Creating sequence and location files... | |||
<<<WARNING>>> This index can only be generated in external memory. | |||
Proceeding, with --external-memory-prefix='gemhg18' | |||
done. | |||
Computing BWT in external memory (likely to take very long)... | |||
</pre> | |||
Revision as of 04:41, 3 November 2010
Does polyphen discard the stop codon ? Testing polyphen with a stop codon: chr22:40053278 C/G should create a stop codon UA.G
Hadoop
download from http://apache.multidist.com//hadoop/core/stable/hadoop-0.20.2.tar.gz
scp on server 2,3,4
Testing GEM
cf:
- http://sourceforge.net/apps/mediawiki/gemlibrary/index.php?title=The_GEM_library
- http://sourceforge.net/apps/mediawiki/gemlibrary/index.php?title=Gem_mapper_man_page
- http://sourceforge.net/apps/mediawiki/gemlibrary/index.php?title=Installation_instructions
downloaded binaries for linux from SF.net
$ ls gem-2-sam gem-do-index_fm_dna_64b gem-mappability gem-mapper gem-split-mapper gem-do-bwt_32b gem-do-index_fm_general_32b gem-mappability_fm_dna_32b gem-mapper_fm_dna_32b gem-split-mapper_fm_dna_32b gem-do-bwt_64b gem-do-index_fm_general_64b gem-mappability_fm_dna_64b gem-mapper_fm_dna_64b gem-split-mapper_fm_dna_64b gem-do-dna-bwt gem-dump-magic gem-mappability_fm_general_32b gem-mapper_fm_general_32b gem-split-mapper_fm_general_32b gem-do-index gem-fasta2loc_cont_32b gem-mappability_fm_general_64b gem-mapper_fm_general_64b gem-split-mapper_fm_general_64b gem-do-index_fm_dna_32b gem-fasta2loc_cont_64b gem-mappability-retriever gem-retriever
Creating an index
( http://sourceforge.net/apps/mediawiki/gemlibrary/index.php?title=Gem_do_index_man_page )
gem-do-index -i ${HG18} -o gemhg18
Welcome to GEM-do-index build 156 (beta) - (2009/10/07 02:50:12 GMT)
(c) 2008-2010 Paolo Ribeca <paolo.ribeca@gmail.com>
************************************************************************
* WARNING: this is a beta version, provided for testing purposes only; *
* check for updates at <http://www.paoloribeca.net/software/GEM>. *
************************************************************************
Creating sequence and location files...
<<<WARNING>>> This index can only be generated in external memory.
Proceeding, with --external-memory-prefix='gemhg18'
done.
Computing BWT in external memory (likely to take very long)...
