Missing output for multiple input bam files in featureCounts
Dear Wei Shi,
I use featureCounts v1.5.0-p1 for 3 input sorted bam files:
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 3 BAM files 1 unknown file ||
|| ? CORE ||
|| P sorted1.bam ||
|| P sorted2.bam ||
|| P sorted3.bam ||
|| ||
|| Output file : /out/ALL.featureCounts.txt ||
|| Annotations : /ref/All_assembled.merged.gtf ||
|| Assignment details : <input_file>.featureCounts ||
|| ||
|| Threads : 6 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Strand specific : inversed ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| Read orientations : fr ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : not required ||
|| ||
Although the output summary file shows the statistics for all 3 files as expected, the output featureCounts.txt file shows the counts for only the first 2 files, and the names of the last 2 files are not separated by tab in the top row:
Geneid Chr Start End Strand Length sorted1.bam sorted2.bamsorted3.bam
ENSG00000278066 KI270731.1 26533 27138 - 606 0 0
ENSG00000277374 KI270750.1 148668 148843 + 176 0 0
ENSG00000273532 KI270721.1 51722 51792 + 71 0 0
ENSG00000276351 KI270721.1 52666 52734 + 69 0 0
ENSG00000275661 KI270721.1 52895 53010 + 116 0 0
ENSG00000277856 KI270726.1 26241 26534 + 294 0 0
ENSG00000275063 KI270726.1;KI270726.1 41444;41572 41489;41876 +;+ 351 0 0
ENSG00000275987 KI270713.1 30437 30580 - 144 0 0
ENSG00000277475 KI270713.1 31698 32528 - 831 1 0
ENSG00000268674 KI270713.1 35407 35916 + 510 0 0
Could you please let me know how I can get the featureCounts.txt summarizing all 3 input files?
Many thanks!
Best wishes,
Yuqia
Dear Wei Shi,
I use featureCounts v1.5.0-p1 for 3 input sorted bam files:
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 3 BAM files 1 unknown file ||
|| ? CORE ||
|| P sorted1.bam ||
|| P sorted2.bam ||
|| P sorted3.bam ||
|| ||
|| Output file : /out/ALL.featureCounts.txt ||
|| Annotations : /ref/All_assembled.merged.gtf ||
|| Assignment details : <input_file>.featureCounts ||
|| ||
|| Threads : 6 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Strand specific : inversed ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| Read orientations : fr ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : not required ||
|| ||
Although the output summary file shows the statistics for all 3 files as expected, the output featureCounts.txt file shows the counts for only the first 2 files, and the names of the last 2 files are not separated by tab in the top row:
Geneid Chr Start End Strand Length sorted1.bam sorted2.bamsorted3.bam
ENSG00000278066 KI270731.1 26533 27138 - 606 0 0
ENSG00000277374 KI270750.1 148668 148843 + 176 0 0
ENSG00000273532 KI270721.1 51722 51792 + 71 0 0
ENSG00000276351 KI270721.1 52666 52734 + 69 0 0
ENSG00000275661 KI270721.1 52895 53010 + 116 0 0
ENSG00000277856 KI270726.1 26241 26534 + 294 0 0
ENSG00000275063 KI270726.1;KI270726.1 41444;41572 41489;41876 +;+ 351 0 0
ENSG00000275987 KI270713.1 30437 30580 - 144 0 0
ENSG00000277475 KI270713.1 31698 32528 - 831 1 0
ENSG00000268674 KI270713.1 35407 35916 + 510 0 0
Could you please let me know how I can get the featureCounts.txt summarizing all 3 input files?
Many thanks!
Best wishes,
Yuqia
Originally posted by shi
View Post
Comment