Question

tximeta doesn't work downloading the ref genome

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rafaelsolersanblas ▴ 50

@rafaelsolersanblas-22935

Last seen 3.0 years ago

Alicante

I have done the command:

 tximeta(coldata)

but while the .gft was been downloaded, I interrupted the process halfway and then it won't let me download the gtf again or move forward:

importing quantifications
reading in files with read_tsv
1 
found matching transcriptome:
[ Ensembl - Mus musculus - release 99 ]
loading existing EnsDb created: 2020-02-17 13:55:01
Error: Could not connect to database:
unable to open database file

What should I do? Thanks

deseq2 tximeta tximport rnaseq • 1.3k views

ADD COMMENT • link 4.8 years ago rafaelsolersanblas ▴ 50

score 0 · Answer 1 · 2020-02-17

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Michael Love 42k

@mikelove

Last seen 2 hours ago

United States

Thanks,

there was another use who had a similar issue:

https://support.bioconductor.org/p/127814/

I will add some details to the vignette, as it sounds like this will happen to users every now and then, and one needs to know how to navigate the BiocFileCache to remove the entry.

ADD COMMENT • link 4.8 years ago Michael Love 42k

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Hi Michael! Thank you for the answer , but I still don't understand how to deal with the problem. I have look inside the directory of BiocFileCache and I have not seen any file with the extension .gtf. Thanks for the help.

ADD REPLY • link 4.8 years ago rafaelsolersanblas ▴ 50

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I try to download the BiocFileCache and this was the message:

Error in fetch(key) : 
  lazy-load database '/home/victor/R/x86_64-pc-linux-gnu-library/3.6/BiocFileCache/help/BiocFileCache.rdb' is corrupt

ADD REPLY • link 4.8 years ago rafaelsolersanblas ▴ 50

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Can you post all code?

Is this the error message you obtain when you run:

bfc <- BiocFileCache()

?

ADD REPLY • link 4.8 years ago Michael Love 42k

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I've made it work somehow, first I have downloaded "dbplyr", and later I could finally load the library "BiocFileCache". With that, I have seen this:

bfcinfo()
# A tibble: 2 x 10
  rid   rname             create_time     access_time     rpath                               rtype   fpath    last_modified_t… etag  expires
  <chr> <chr>             <chr>           <chr>           <chr>                               <chr>   <chr>               <dbl> <chr>   <dbl>
1 BFC1  gencode.v27.anno… 2020-02-17 11:… 2020-02-17 11:… /home/victor/.cache/BiocFileCache/… relati… 10cc7de…               NA NA         NA
2 BFC2  Mus_musculus.GRC… 2020-02-17 13:… 2020-02-17 13:… /home/victor/.cache/BiocFileCache/… relati… 29cb720…               NA NA         NA

So, I have removed the file like this:

> bfcremove(rids = "BFC2")
> > bfcinfo()
> # A tibble: 1 x 10   rid   rname             create_time     access_time     rpath                               rtype   fpath   
> last_modified_t… etag  expires   <chr> <chr>             <chr>        
> <chr>           <chr>                               <chr>   <chr>     
> <dbl> <chr>   <dbl> 1 BFC1  gencode.v27.anno… 2020-02-17 11:…
> 2020-02-17 11:… /home/victor/.cache/BiocFileCache/… relati… 10cc7de…  
> NA NA         NA

Now it works properly, thank you Michael! :) Can I ask you another issue? How can I import several quant.sf in the same file to do the import with Tximeta? I understand with only one, but I don't if I have several quant.sf files.

ADD REPLY • link 4.8 years ago rafaelsolersanblas ▴ 50

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tximeta and tximport (which it builds upon) are both designed for importing multiple files (importing one file is a special case really).

See:

?tximeta

the first argument describes a data.frame with two columns, files and names. You can have a single row and just import one file, or multiple rows of this data.frame.

ADD REPLY • link 4.8 years ago Michael Love 42k

score 0 · Answer 2 · 2020-02-18

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rafaelsolersanblas ▴ 50

@rafaelsolersanblas-22935

Last seen 3.0 years ago

Alicante

Okay! Thanks Michael :)

ADD COMMENT • link 4.8 years ago rafaelsolersanblas ▴ 50