Can't find output after featureCounts

Question

[ovariohisterectomia]

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.                                         ||
||                                                                            ||
\\============================================================================//

[GenoMax]

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 for R equivalent.

[Benn]

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?

head(newcount)

[ovariohisterectomia]

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!

16645 id17504 NW_020170478.1 163493 164078 + 586 16646 id17505 NW_020170478.1 164152 165183 + 1032 16647 id17506 NW_020170478.1 165276 165355 + 80 16648 id17507 NW_020170478.1 172550 172942 + 393 16649 id17508 NW_020170478.1 188955 188993 - 39 16650 id17509 NW_020170478.1 188819 188929 - 111 16651 id17510 NW_020170478.1 188703 188770 - 68 16652 id17511 NW_020170478.1 188550 188665 - 116 16653 id17512 NW_020170478.1 188356 188512 - 157 16654 id17513 NW_020170478.1 187988 188278 - 291 16655 id17514 NW_020170478.1 187394 187729 - 336 16656 id17515 NW_020170478.1 186212 186470 - 259 16657 id17516 NW_020170478.1 185861 185919 - 59 16658 id17517 NW_020170478.1 184551 184810 - 260 16659 id17518 NW_020170478.1 184350 184461 - 112 16660 id17519 NW_020170478.1 184119 184233 - 115 16661 id17520 NW_020170478.1 183337 183455 - 119 16662 id17521 NW_020170478.1 182627 182738 - 112 16663 id17522 NW_020170478.1 182452 182542 - 91 16664 id17523 NW_020170478.1 182273 182372 - 100 16665 id17524 NW_020170478.1 182085 182219 - 135 16666 id17525 NW_020170478.1 181977 182010 - 34 [ reached 'max' / getOption("max.print") -- omitted 58598 rows ]

$targets [1] "H1.1sorted.bam"

$stat Status H1.1sorted.bam 1 Assigned 24019924 2 Unassigned_Unmapped
0 3 Unassigned_Read_Type 0 4
Unassigned_Singleton 0 5 Unassigned_MappingQuality
0 6 Unassigned_Chimera 0 7
Unassigned_FragmentLength 0 8
Unassigned_Duplicate 0 9 Unassigned_MultiMapping
0 10 Unassigned_Secondary 0 11
Unassigned_NonSplit 0 12 Unassigned_NoFeatures
5440071 13 Unassigned_Overlapping_Length 0 14
Unassigned_Ambiguity 4438077

Answer 1

[ATpoint]

It is in newcount as you redirected the output to that variable. Please spend some time on the R basics before diving into analysis.

Answer 2

[ovariohisterectomia]

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