I have some .bam files and I also got featureCounts by Subread. But after getting the featureCounts I realized that among my bam files 2 of them actually belong to the same sample. So I wonder if I can remove the result of these two and after merging bam files add them again into featureCounts without doing all the featureCounts for other samples again.

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    $\begingroup$ Sure, paste and company will help or load it into R and cbind stuff as needed, but seriously, featureCounts is blazingly fast and even with many samples on a modest laptop it just takes minutes. Just rerun it. Given the 59min period of time that this question is here it would have been finished by now probably ;-) For code suggestions it is mandatory to add example data though. $\endgroup$
    – ATpoint
    Jul 30 at 12:59
  • $\begingroup$ It sounds like you are supplying multiple BAMs to featureCounts, while this is possible I think it's better to run featureCounts on each BAM separately and then use a Python script or cbind function in R as mentioned above to combine the results of multiple samples. This shall give you more flexibility. $\endgroup$
    – Phoenix Mu
    Jul 30 at 21:35
  • $\begingroup$ Yeah thanks for the answers. As ATpoint mentioned I realized that featureCounts doesn't need much computational power and time. And good to know I can merge with Python or R script. $\endgroup$ Jul 30 at 21:43

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