User:Lindenb/Notebook/UMR915/20101104

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SOAPAligner

testing soap aligner:

 soap2.20release/soap -a xx_3_1.fastq.gz -bxx_3_2.fastq.gz -D hg18.fa.index -o ~/soap_results.data -2 ~/unpaired.data
 File Error: unrecognized file

hum... it doesn't like the gzipped fastq ?... :-/ unzippinf...

/usr/local/package/soap2.20release/soap -a XX_3_1.fastq -b XX_3_2.fastq -D hg18.fa.index -o soap_results.data -2 unpaired.data -m 200 -x 600

Begin Program SOAPaligner/soap2
Thu Nov  4 11:18:24 2010
Reference: hg18.fa.index
Query File a: 4366_3_1.fastq
Query File b: 4366_3_2.fastq
Output File: soap_results.data
             unpaired.data
Load Index Table ...
Load Index Table OK
Begin Alignment ...
131072 ok   86.16 sec
262144 ok   84.23 sec
393216 ok   93.31 sec
524288 ok   90.48 sec
(...)

GEM

> gem-mapper
Welcome to GEM-mapper build 544 (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>.     *
************************************************************************
Names of index, input and output file are mandatory
Usage:
 gem-mapper
  -I <index_prefix>               (mandatory)
  -c|--colorspace                 (index is colorspace-encoded)
  -e|--emulate-complement         (for indices lacking it)
  -i <input_file>                 (mandatory, FASTA or FASTQ)
  -q|--quality-format 'ignore'|'phred'|'solexa'
                                  (mandatory with FASTQ input)
  --reads-per-block <number>      (default=10000)
  -o <output_prefix>              (mandatory)
  -t <thread_number>              (default=1)
  -m <max_mismatch_number>        (default=2)
  --mismatch-alphabet <symbols>   (default="ACGT")
  -Q|--quality-model 'gem'|'flat' (default='gem')
  --gem-quality-threshold <number>
                                  (default=26, that is e<=2e-3)
  -d|--decoding-threshold 'all'|<number>
                                  (default=10)
  --filtering-threshold <number>  (default=40)
  --max-indel-length <number>     (default=5)
  --disable-accelerators          (for debugging purposes)
  -h|--help                       (print usage)

no paired-end sequencing ?

gem-mapper -i XXXX_1.fastq -o gemout -I gemhg18 -q phred