[Useq-users] Problems making splice junction library file

[James P. <jim...@gm...>]

Hi all,

I'm having problems building the splice junction library file, following
the isntructions given here: http://useq.sourceforge.net/usageRNASeq.html

I'm at the: Create a multi-fasta file containing extended splice junctions
matched to your target read length minus 4bp using the USeq
MakeTranscriptome app. part

Steps one and two go ok.

However when I try to run MakeTranscriptome I get lots of errors.

Specifically:


Error parsing UCSCGeneLine name2 #name chrom strand txStart txEnd cdsStart
cdsEnd exonCount exonStarts exonEnds

Error parsing UCSCGeneLine ENSRNOG00000018674 ENSRNOT00000050151 chr1 -
133925529 134302139 133925682 134302088 19
133925529,133932969,133938113,133959565,133978443,133981901,133991271,134081434,134169351,
134170342,134172615,134178756,134179501,134180032,134181232,134196669,134237566,134238370,134301840,
133925868,133933128,133938155,133959640,133978687,133982074,133991402,134081623,134169454,134170407,1341
72639,134179053,134179643,134180175,134181390,134196738,134237638,134238445,134302139,

repeated

....

I also get to stderr:

java.lang.NumberFormatException: For input string: "strand"
        at
java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
        at java.lang.Integer.parseInt(Integer.java:481)
        at java.lang.Integer.parseInt(Integer.java:514)
        at util.bio.parsers.UCSCGeneLine.<init>(UCSCGeneLine.java:62)
        at
util.bio.parsers.UCSCGeneModelTableReader.parseGeneTableFile(UCSCGeneModelTableReader.java:335)
        at
util.bio.parsers.UCSCGeneModelTableReader.<init>(UCSCGeneModelTableReader.java:38)
        at
util.bio.seq.MakeTranscriptome.processArgs(MakeTranscriptome.java:548)
        at util.bio.seq.MakeTranscriptome.<init>(MakeTranscriptome.java:33)
        at util.bio.seq.MakeTranscriptome.main(MakeTranscriptome.java:514)

repeated

.......

which seems strange, it seems as though it doesn't like the - or + perhaps?

Anyone seen this error before? Many thanks in advance for any help you can
give.

The command I am running is:

java -jar ../../progs/USeq_7.9.5/Apps/MakeTranscriptome -f
../rat/genome_fastas/ -u ../genetabs/geneTable.PSC.xls -r 30 1> stdout.txt
2>  stderr.txt

Jim