text: user1369: I used this command for extracting read counts for almost 60 samples using featureCounts.
  featureCounts -a /gencode.v27.primary_assembly.annotation_nochr.gtf -F GTF -p -s 2 -T 8 -o counts.txt sample.sorted.bam
  
  I see many "temp-core-100373-A4BF0116E148.sam-TH00-BK004414.tmp" files like this dumped in my directory. I'm able to delete them only manually. Is there a way to get rid of these tmp files from my directory while using the command?
  
  user77: You shouldn't delete them while featureCounts is running, it's creating read-name-sorted temporary files so it can more easily look at both mates together. Just wait for it to finish running and it will clean up the files itself. Doing so beforehand is liable to cause an error.
  
original_text: 1369: <p>I used this command for extracting read counts for almost 60 samples using featureCounts.</p>
  
  <pre><code>featureCounts -a /gencode.v27.primary_assembly.annotation_nochr.gtf -F GTF -p -s 2 -T 8 -o counts.txt sample.sorted.bam
  </code></pre>
  
  <p>I see many "temp-core-100373-A4BF0116E148.sam-TH00-BK004414.tmp" files like this dumped in my directory. I'm able to delete them only manually. Is there a way to get rid of these tmp files from my directory while using the command?</p>
   77: <p>You shouldn't delete them while featureCounts is running, it's creating read-name-sorted temporary files so it can more easily look at both mates together. Just wait for it to finish running and it will clean up the files itself. Doing so beforehand is liable to cause an error.</p>
  