Are there any documentation and tutorials for the KNIME 4Bio and NGS nodes?

Question

[valentina_stepanenko]

Are there any documentation and tutorials for the KNIME 4Bio and NGS nodes? Have you tried it?

[Pierre Lindenbaum]

Hi Valentina, I'm the author of knime4bio. While my colleagues are still using it to process VCF data, I consider that knime4bio is now deprecated (old VCF specification, loss of metadata from the VCF header ) and I'm working one something more useful. However, you can still use the basic knime.org for processing large VCF tables, it's always better than using Excel. Other alternatives are using galaxy, learning the command line, etc...

[valentina_stepanenko]

thx, how to install it, and tell how to input data therein like in all NGS KNIME nodes? That node can be useful, so put a better youtube video with a detailed explanations and audio, pls.

[Pierre Lindenbaum]

how to install it

everything has moved when google has closed code.google.com https://github.com/lindenb/knime4bio/wiki/Install

it won't work with knime 3

how to input data

has I said , the nodes are deprecated. You can still upload a VCF without knime4bio using IO/file loader/skip kines starting with '##'/read header/use tab as delimiter

[valentina_stepanenko]

Do you know how to input data into there NGS Knime 3 nodes? thanks

[GenoMax]

Please use ADD REPLY/ADD COMMENT to respond to existing posts. SUBMIT ANSWER should be used only for new answers to the original question.

[Pierre Lindenbaum]

define "data" please.

[valentina_stepanenko]

fastq, vcf, bam, sam files. I finally found a FASTQ reader node and it reads OK (has green color and executes). However, the output of it can`t go to the next FASTQ Qualiti Stats NGS node. I need a tutorial and a cookbook on KNIME bioinformatics nodes. thx.