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icSHAPE pipeline

Perl 100.00%

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icshape's Issues

Path to adapter in configuration file

Default path to adapter file is not working
ADAPTER $ICSHAPE/data/TruSeq2-PE.fa
should be
ADAPTER $ICSHAPE/data/adapter/TruSeq2-PE.fa

no "shape2Bedgraph.pl" in scripts directory

there is one code "SHAPE2BEDGRAPGH $ICSHAPE/scripts/shape2Bedgraph.pl" in the configure file, no "shape2Bedgraph.pl" file in scripts directory.

Can you upload final icSHAPE.out file?

Hi,

Can you upload full transcriptome version of the final icSHAPE.out file from the samples processed in the paper? The one in the test directory seems to have data for just one identifier. If you could also upload the file you use for genome browser visualization that would also be great.

Thanks!

Prisca

Can I know the Bowtie2 options you have used?

Hi @qczhang , this is Bo Li from UC Berkeley. We are working on some experiments using your icSHAPE data published in Nature. Can you let me know the Bowtie 2 options you have used so that we can repeat your experiments? In particular, we are interested in the options for generating "up to ten random hits".

Thanks a lot!
Bo

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