Rsubread unable to return alignments
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Daniel • 0
@daniel-24295
Last seen 8 months ago

So i've been trying to do some alignments with Rsub and every time i run it, only aligns one file and it doesn't do the rest. I have been running the latest version of everything, R( 4.0) Rsubread is 2.4.2 and BiocManager 1.30.10 The following code is from a tutorial for RNA-seq analysis but because of this problem, I can't replicate Code should be placed in three backticks as shown below

align(index="data/chr1_mm10",readfile1=fastq.files)



# //================================= setting ==================================\\
||                                                                            ||
|| Function      : Read alignment (RNA-Seq)                                   ||
|| Input file    : SRR1552444.fastq.gz                                        ||
|| Output file   : SRR1552444.fastq.gz.subread.BAM (BAM)                      ||
|| Index name    : chr1_mm10                                                  ||
||                                                                            ||
||                    ------------------------------------                    ||
||                                                                            ||
||                               Threads : 1                                  ||
||                          Phred offset : 33                                 ||
||                             Min votes : 3 / 10                             ||
||                        Max mismatches : 3                                  ||
||                      Max indel length : 5                                  ||
||            Report multi-mapping reads : yes                                ||
|| Max alignments per multi-mapping read : 1                                  ||
||                                                                            ||
\\============================================================================//

//================= Running (02-Dec-2020 17:42:55, pid=4696) =================\\
||                                                                            ||
|| Check the input reads.                                                     ||
|| The input file contains base space reads.                                  ||
|| Initialise the memory objects.                                             ||
|| Estimate the mean read length.                                             ||
|| The range of Phred scores observed in the data is [2,41]                   ||
|| Create the output BAM file.                                                ||
|| Check the index.                                                           ||

The index was built by using an old version of Subread; its format is no longer supported. Please use the current version of the index builder to rebuild it.
# please also include the results of running the following in an R session 

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Rsubread_2.4.2 edgeR_3.32.0   limma_3.46.0  

loaded via a namespace (and not attached):
[1] compiler_4.0.2  Matrix_1.2-18   tools_4.0.2     Rcpp_1.0.5      tinytex_0.27    grid_4.0.2     
[7] locfit_1.5-9.4  xfun_0.19       lattice_0.20-41

Does anybody has an idea? ?I have 12 samples and it only returns one Thanks

Rsubread Alignment • 278 views
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Hi, Dan, I tried in my macOS to build a human chr1 index then map a small sample, and it was all done with no errors/warnings. In your case, because the align() function encountered an index problem, it stopped running, so the remaining 11 samples were not processed.

Can you try this:

$ hexdump -C data/chr1_mm10.00.b.tab | head -n 20

, and copy the results here. This can tell if your index was correctly built.

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Wei Shi ★ 3.3k
@wei-shi-2183
Last seen 4 hours ago
Australia/Melbourne/Olivia Newton-John …

As the screen output indicates, the index you used for mapping was generated from an older version and it is not supported anymore. So could you please regenerate your index using the buildindex function and then rerun your mapping to see if the problem will be resolved?

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Thanks so much for your help Wei She I used the same new version of Rsubread for the buildindex this is the coding

buildindex(basename="chr1_mm10",reference="chr1.fa")

Thanks so much Dan

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