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Question: Using sluth with Salmon data, error while sleuth_prep
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gravatar for Walter F. Baumann
12 days ago by
Walter F. Baumann 10 wrote:

Hi,
I want to use sleuth on the data salmon returned. In the first step, because sleuth needs actually kallisto, I used wasabi to generate the abundance.h5 file. However, after using

so <- sleuth_prep(s2c, ~ condition, num_cores = 1)


(s2c looks like that: )

sample condition
1 sample1         D
2 sample2         D
3 sample3         D
4 sample4         C
5 sample5         C
6 sample6         C
                                                                                   path
1 path/to/folder/sample1
2 path/to/folder/sample2

2 path/to/folder/sample3

2 path/to/folder/sample4

2 path/to/folder/sample5

2 path/to/folder/sample6

 

 

I get the following error:

reading in kallisto results
dropping unused factor levels
......
normalizing est_counts
117728 targets passed the filter
normalizing tpm
merging in metadata
summarizing bootstraps
.Error in process_bootstrap(i, samp_name, kal_path, num_transcripts, est_counts_sf[[i]],  :
  File h5 has no bootstraps.Please generate bootstraps using "kallisto quant -b".File Y:/AG_Huebner/Eric/tmp_for_jobs/seq_polyA_trim/hs_li_001_D_mR_tr_clean.fastq.gz_quant/abundance.h5 has no bootstraps.Please generate bootstraps using "kallisto quant -b".

 

My session Info:

Session info --------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.4.2 (2017-09-28)
 system   i386, mingw32               
 ui       RStudio (1.1.383)           
 language (EN)                        
 collate  English_United States.1252  
 tz       Europe/Berlin               
 date     2017-11-07
ADD COMMENTlink modified 12 days ago • written 12 days ago by Walter F. Baumann 10
2

sleuth and wasabi are not Bioconductor software, and so this support site isn't the best place to post questions about use of these software.

Here is the support forum for Sleuth:

https://groups.google.com/forum/#!forum/kallisto-sleuth-users

And you could post wasabi questions here:

https://github.com/COMBINE-lab/wasabi

ADD REPLYlink written 12 days ago by Michael Love14k

Hello Walter,

I am trying to adopt the salmon > wasabi > sleuth pipeline and have just run into the very same problem. I've started the topic in wasabi github site. Feel free to join there. Would be great to solve this issue and move on.

Best,

Karel

ADD REPLYlink written 11 days ago by muller0

Hi, first of all thanks for moving this discussion. There is a bootstrap mode (--numBootstraps)in salmon and this added information that is needed by wasabi. I set it on 10. The bootstraps are needed to estimate the technical variance in your sample, which is needed by sleuth (and I guess this is what makes sleuth special compared to DESeq2 and edgeR) (according to the manual).

 

ADD REPLYlink modified 10 days ago • written 10 days ago by Walter F. Baumann 10
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