Kallisto output

11 views
Skip to first unread message

Siawpeng Er

unread,
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

unread,
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:
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


--
You received this message because you are subscribed to the Google Groups "Alternative Splicing and Functional Prediction" group.
To unsubscribe from this group and stop receiving emails from it, send an email to alt_predictio...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/alt_predictions/56ebccb7-b43c-465d-a2e8-dd059f819768n%40googlegroups.com.
Reply all
Reply to author
Forward
0 new messages