Hello, I have been having an issue with this function featureCounts() for reads summarize.
I want to make an analysis from exons. Everything worked fine until now, but seems like I cant give the input .bam files in a right way. Im getting a error:
Script:
Output:
I also tried to make the character vector manually, no success.
Tried getting the exact path from bash, no success.
Wrote the file one by one manually on featureCounts line, no success.
Checked the files were correctly BAM already.
To be honest Im getting out of ideas and I dont want to loose another evening with this issue, it seems like a detail.
Do you see the problem?
Thanks in advance.
UPDATE: I have tried with
, again without success :/
I want to make an analysis from exons. Everything worked fine until now, but seems like I cant give the input .bam files in a right way. Im getting a error:
Script:
Code:
setwd(where/bam/files/are/located) fls <- dir(full.names = TRUE ) fc1 <- featureCounts(files = fls, annot.ext = "/home/.../tomics/data2", isGTFAnnotationFile = TRUE, GTF.featureType = "exon", GTF.attrType = "gene_id")
ERROR: invalid parameter: './16_GCCAAT_L002_R1_001.bam'
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file './.Rsubread_featureCounts_pid2638': No such file or directory
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file './.Rsubread_featureCounts_pid2638': No such file or directory
Tried getting the exact path from bash, no success.
Wrote the file one by one manually on featureCounts line, no success.
Checked the files were correctly BAM already.
To be honest Im getting out of ideas and I dont want to loose another evening with this issue, it seems like a detail.
Do you see the problem?
Thanks in advance.
UPDATE: I have tried with
Code:
featureCounts -t exon -g gene_id -a data2.gtf -o counts.txt 4_GCCAAT_L001_R1_001.bam 8_AGTTCC_L001_R1_001.bam 16_GCCAAT_L002_R1_001.bam 20_AGTTCC_L003_R1_001.bam 28_GCCAAT_L004_R1_001.bam 32_AGTTCC_L004_R1_001.bam 40_GCCAAT_L005_R1_001.bam 44_AGTTCC_L006_R1_001.bam
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