Kallisto output

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Siawpeng Er

Oct 12, 2020, 1:03:10 PM10/12/20
to Alternative Splicing and Functional Prediction

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

Oct 12, 2020, 2:32:22 PM10/12/20
to Alternative Splicing and Functional Prediction, espp...@gmail.com
Hi Siawpeng,

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

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?


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