Trim - Cannot trim to large positions

1

I have a (gapped) FASTA file from a MSA output with about 10 sequences each of length 698. I’m trying to trim the sequences and keep only the sequence at positions to 368 and 445.

However, when I use the following inputs the entire sequence is gone in the output.

  • Trim this column only: 0
  • Trim from the beginning up to this position: 368
  • Remove everything from this position to the end : 445
  • Is input dataset in FASTQ format?: No
  • Ignore lines beginning with these characters: >

I also tried trimming beginning to position 100 and position 0 to end, and also got back no sequences. When I changed the 100 to 10, the trimming worked. Is there a maximum number of characters I can trim or am I doing something wrong?

I also tried trim sequences tool, but I got an error because the gaps were invalid nucleotide sequences.

Any advice or suggestions would be much appreciated, thanks!

2

Hi @vant

There shouldn’t be a hard limit with any trimming tool as far as I know. However, the parameter logic you are using might need some tuning. We can help with that here. I can’t tell which exact tool and version you are running right now.

Would you like to share your history? It would be helpful to test out the queries with your actual data, plus to double check that formats are OK for this tool. You could list out a few of the datasets associated with your observations. Try to leave all the inputs and error datasets intact please.

And if the tool just needs more memory allocated, we can help to diagnose that and maybe solve it (with alternatives or even asking admins to add more resources!).

How to share is in the banner topic, also here → How to get faster help with your question

Let’s start there! :slight_smile: