Hi everyone. Im an absolutely new guy working in bioinformatics, and i would like if you could help me.
I want to do featurecounts, i think im doing it well but i cant find the output...i was reading that i should expect a kind of table with my data, but i cant find it...do i need an "extra line "?
this is what i did... Thank you in advance
> newcount = featureCounts(files=c("H1_1sorted.bam"), annot.ext="GCF_000524195.1_ASM52419v1_genomic.gff", isGTFAnnotationFile=TRUE, isPairedEnd=TRUE, GTF.attrType="ID")
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.0.0
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o H1_1sorted.bam ||
|| ||
|| Annotation : GCF_000524195.1_ASM52419v1_genomic.gff (GTF) ||
|| Dir for temp files : . ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : not required ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file GCF_000524195.1_ASM52419v1_genomic.gff ... ||
|| Features : 75264 ||
|| Meta-features : 75264 ||
|| Chromosomes/contigs : 572 ||
|| ||
|| Process BAM file H1_1sorted.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 33898072 ||
|| Successfully assigned alignments : 24019924 (70.9%) ||
|| Running time : 2.16 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
•
written
by
ovariohisterectomia •
2 answers
Than you all. I solved it.
as you told, the "newcount" was the name of the new file. And with the command
head(newcount)
im able to see the counts. Now i "printed" the output to a .txt file with
write.table(x=data.frame(newcount$annotation[,c("GeneID","Length")],newcount$counts,stringsAsFactors=FALSE),file="newcount.txt",quote=FALSE,sep="\t",row.names=FALSE)
Thankyou every one for your answers
SOLVED
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Looks like you forgot to provide an output file to hold the result table. You would normally provide this with
-o <output_file>on command line version. Look forRequivalent.I have never used the program in R, but I think your reads counts table will be saved in R object
newcount. Can you check that object with e.g. head?thank you Benn for your answer (and thanks to genomax too). When i write that command , there is a long list and finally sent me a message ...is there any way to export that to an .xls file or something? This is what i get ... thank you!