# filter.seqs removing sequences from the fasta file?

**URL:** <https://forum.mothur.org/t/filter-seqs-removing-sequences-from-the-fasta-file/1957>\
**Category:** Commands in mothur\
**Created:** [August 1, 2014, 10:55am UTC](https://forum.mothur.org/t/filter-seqs-removing-sequences-from-the-fasta-file/1957 "2014-08-01T10:55:26Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![svazquez](https://avatars.discourse-cdn.com/v4/letter/s/f6c823/32.png) [@svazquez](https://forum.mothur.org/u/svazquez)\
**Post date:** [August 1, 2014, 10:55am UTC](https://forum.mothur.org/t/filter-seqs-removing-sequences-from-the-fasta-file/1957/1 "2014-08-01T10:55:26Z")

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Hi

I am processing a downsampled dataset to find the best parameters for my analysis.  
After running screen.seqs I ended up with:

# of unique seqs: 8794

total # of seqs: 10129

Then, I ran  
mothur \> filter.seqs(fasta=454downsample.shhh.trim.unique.good.align, vertical=T, trump=., processors=2)

and the output was:  
Length of filtered alignment: 1219  
Number of columns removed: 48781  
Length of the original alignment: 50000  
Number of sequences used to construct filter: 7372

Someone can explain why filter.seqs started with 8749 unique seqs but ended up in a fasta file with 7372 seqs? I thought that filter.seqs would only remove common gaps and missing data but not sequences!

Thanks!

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<div class="post-metadata">

**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [August 1, 2014, 8:32pm UTC](https://forum.mothur.org/t/filter-seqs-removing-sequences-from-the-fasta-file/1957/2 "2014-08-01T20:32:21Z")

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I suspect the data you posted were from running summary.seqs on 454downsample.shhh.trim.unique.align and not 454downsample.shhh.trim.unique.good.align

Pat