Kallisto output

[Siawpeng Er]

I have error at the last stage of the kallisto analysis. I use all of the default parameters to test running, excpet for changing minimum number of cell differrent=2

Predicted sample export failed..    

sample_index_list = map(lambda x: values.index(x), filter_names)

ValueError: '8_S2_L003_001..1.bed' is not in list.

May I know any possible solution for it? Thanks

[Nathan Salomonis]

Hi Siawpeng,

There is a log file produced for each fastq file pair when processed saved to the output directory in the folder:

ExpressionInput/kallisto/*FASTQ*

Can you see which samples had an:

1) abundance.tsv file

2) .json file

Is there a log.txt file in the ExpressionInput directory? If so, can you send it to me? Which samples are missing an abundance.tsv file. Can you send a representative .json file and abundance.tsv file for the sample which ran and one that only partially ran?

Which operating system, which species and which AltAnalyze version are you using?

Best,

Nathan

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