Checking error in fasta file after running the transcript

Question

[Neo_42]

Hi lovely community,

I just ran a large fasta file of 10,000 transcripts. I want to check if all the transcripts got run successfully. I used this command cut -f1 -d "," filenamexx/xyz.csv | sort | uniq | wc -l to check all the transcripts in the CSV file. The output shows 9990 out of 10,000 transcripts. So 10 transcript is missing. Is any way I can check these 10 missing transcripts? How can I do that? Any help or guidance would be highly appreciated! Thank you!

Answer 1

[ATpoint]

Make a list of transcripts from the original file and sort it (sort -k1,1), same for the output, then use comm

Like:

$ cat original.txt
name1
name2
name3
name4

$ cat output.txt
name1
name3
name4

$ comm -23 original.txt output.txt
name2