Please, could someone help me to export featureCounts (Rsubread) results?
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@gustavoborin01-6892
Last seen 6.9 years ago

Hi everyone,

I'm trying to export the featureCounts output results of Rsubread to a .xls format (excel), but I'm not having success. I have got the counts of the reads from my RNASeq experiment, but I can't export the result. I used the command below, but it did not work. It appears that warning message.

I know the reportReads argument saves my output, but the generated files are so big and I know that exists a different and simpler way to do that. So, really appreciate if someone could help me.

Used function

>featureCounts(file="T_reesei_F24-2_GTGGCC_L008_R1_001.cleanreads.fastq.gz_tophat2/F24h-2_accepted_hits.bam",annot.ext = "TrireRUTC30_1_GeneCatalog_genes_20110526.fix2.gtf",isGTFAnnotationFile = TRUE,GTF.featureType = "CDS",GTF.attrType = "transcript_id")

GTF file

TrireRUTC30_1_scaffold_23 JGI exon 45921 45986 . - . transcript_id "e_gw1.23.89.1"; gene_id "e_gw1.23.89.1"
TrireRUTC30_1_scaffold_23 JGI CDS 44782 45549 . - 0 transcript_id "e_gw1.23.89.1"; gene_id "e_gw1.23.89.1"
TrireRUTC30_1_scaffold_23 JGI CDS 45634 45819 . - 0 transcript_id "e_gw1.23.89.1"; gene_id "e_gw1.23.89.1"

Output results

1664                                         +;+;+   3186
1665                                           +;+    234
1666                                             +   1362
 [ reached getOption("max.print") -- omitted 8186 rows ]

$targets
[1] "T_reesei_F24.2_GTGGCC_L008_R1_001.cleanreads.fastq.gz_tophat2.F24h.2_accepted_hits.bam"

$stat
                      Status
1                   Assigned
2       Unassigned_Ambiguity
3    Unassigned_MultiMapping
4      Unassigned_NoFeatures
5        Unassigned_Unmapped
6  Unassigned_MappingQuality
7 Unassigned_FragementLength
8         Unassigned_Chimera
  T_reesei_F24.2_GTGGCC_L008_R1_001.cleanreads.fastq.gz_tophat2.F24h.2_accepted_hits.bam
1                                                                               34914980
2                                                                                   8021
3                                                                                  88386
4                                                                               11354142
5                                                                                      0
6                                                                                      0
7                                                                                      0
8                                                                                      0

Used command to export

> res <- write.table(res$table, file = "F24.xls")

Warning message

Error in res$counts : object of type 'closure' is not subsettable

 

Thanks Gustavo Borin

rnaseq rsubread featurecounts r • 2.9k views
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2
Entering edit mode
@james-w-macdonald-5106
Last seen 12 hours ago
United States

You have to capture the output of featureCounts(), by assigning it to an object.

counts <- featureCounts(<arguments go here>)

Then if you look at the help for featureCounts, you will see this:

Value:

     A list with the following components:

  counts: a data matrix containing read counts for each feature or
          meta-feature for each library.

And you can write that out to a file.

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2
Entering edit mode
Wei Shi ★ 3.3k
@wei-shi-2183
Last seen 44 minutes ago
Australia/Melbourne/Olivia Newton-John …

Dear Gustavo Borin,

The 'reportReads' argument enables the detailed read assignment results to be saved into a file. The file includes overlapping features and other data for each read (each row corresponds a read). But I don't think that is what you want.

To save read counts generated from featureCounts, try the following command:

fc <- featureCounts(file="T_reesei_F24-2_GTGGCC_L008_R1_001.cleanreads.fastq.gz_tophat2/F24h-2_accepted_hits.bam",annot.ext="TrireRUTC30_1_GeneCatalog_genes_20110526.fix2.gtf",isGTFAnnotationFile = TRUE,GTF.featureType = "CDS",GTF.attrType = "transcript_id")

write.table(x=data.frame(fc$annotation[,c("GeneID","Length")],fc$counts,stringsAsFactors=FALSE),file="counts.txt",quote=FALSE,sep="\t",row.names=FALSE)

The generated 'counts.txt' file is a tab-delimited file which includes gene identifier, gene length and counts for each gene in each library.

Hope this helps.

Wei

 

 

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0
Entering edit mode
@gustavoborin01-6892
Last seen 6.9 years ago

Thank you so much James and Wei Shi. It was so simple to solve it! It worked successully!

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