# screen.seqs and filter.seqs

**URL:** <https://forum.mothur.org/t/screen-seqs-and-filter-seqs/866>\
**Category:** Commands in mothur\
**Created:** [April 17, 2012, 8:27am UTC](https://forum.mothur.org/t/screen-seqs-and-filter-seqs/866 "2012-04-17T08:27:37Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![JamesoK](https://avatars.discourse-cdn.com/v4/letter/j/a88e57/32.png) [@JamesoK](https://forum.mothur.org/u/JamesoK)\
**Post date:** [April 17, 2012, 8:27am UTC](https://forum.mothur.org/t/screen-seqs-and-filter-seqs/866/1 "2012-04-17T08:27:37Z")

</div>

Hi,

I am having some trouble when running screen.seqs and filter.seqs on my 16S seqs after alignment to the SILVA reference alignment.

Here is the summary of my alignment:

Start End NBases Ambigs Polymer NumSeqs  
Minimum: 1044 1103 10 0 2 1  
2.5%-tile: 1044 6332 313 0 4 5658  
25%-tile: 1044 8508 397 0 5 56573  
Median: 1044 9890 424 0 5 113145  
75%-tile: 1044 9994 434 0 5 169717  
97.5%-tile: 1044 10351 454 0 6 220631  
Maximum: 43097 43116 485 0 8 226288  
Mean: 1042.56 9323.6 410.339 0 5.00103

# of unique seqs: 62445

total # of seqs: 226288

Then I ran screen.seqs as follows:

screen.seqs (fasta=2d.shhh.trim.pick.unique.align, name=2d.shhh.trim.pick.names, group=2d.shhh.groups, end=6332, minlength=300, processors=2)

Here is a summary of the output of the screen.seqs command:

Start End NBases Ambigs Polymer NumSeqs  
Minimum: 1044 6332 300 0 3 1  
2.5%-tile: 1044 6388 317 0 4 1485  
25%-tile: 1044 7941 370 0 5 14849  
Median: 1044 9820 412 0 5 29698  
75%-tile: 1044 9914 430 0 5 44546  
97.5%-tile: 1044 10303 455 0 6 57910  
Maximum: 3616 13875 485 0 8 59394  
Mean: 1044.53 8966.52 399.971 0 5.03881

# of Seqs: 59394

Next I ran filter.seqs with the trump command:

filter.seqs(fasta=2d.shhh.trim.pick.unique.good.align, vertical=T, trump=., processors=2)

Here is the summary of the filter.seqs output:

Start End NBases Ambigs Polymer NumSeqs  
Minimum: 1 402 131 0 3 1  
2.5%-tile: 1 404 141 0 3 1485  
25%-tile: 1 404 151 0 4 14849  
Median: 1 404 153 0 4 29698  
75%-tile: 1 404 157 0 5 44546  
97.5%-tile: 11 404 168 0 6 57910  
Maximum: 26 404 194 0 8 59394  
Mean: 2.87526 404 154.161 0 4.32683

# of Seqs: 59394

As you can see, I am losing a lot of length after running the filter command! Is there any way I might improve on this so that I can keep around 300-400 bases of the alignment whilst not reducing my total no. of sequences too much? Any advice would be much appreciated and I apologise for the long post!

Many 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:** [April 18, 2012, 12:18pm UTC](https://forum.mothur.org/t/screen-seqs-and-filter-seqs/866/2 "2012-04-18T12:18:44Z")

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Hi,

The problem is…

> Start End NBases Ambigs Polymer NumSeqs  
> Minimum: 1044 6332 300 0 3 1  
> 2.5%-tile: 1044 6388 317 0 4 1485  
> 25%-tile: 1044 7941 370 0 5 14849  
> Median: 1044 9820 412 0 5 29698  
> 75%-tile: 1044 9914 430 0 5 44546  
> 97.5%-tile: 1044 10303 455 0 6 57910  
> Maximum: 3616 13875 485 0 8 59394  
> Mean: 1044.53 8966.52 399.971 0 5.03881
> 
> # of Seqs: 59394

The "Maximum line indicates that you have a sequence that starts at 3616, ends after 6332 and is longer than 300 bp. So essentially, you’re only going to be looking at the bases that run between positions 3616 and 6332. How about trying this instead?

  
screen.seqs (fasta=2d.shhh.trim.pick.unique.align, name=2d.shhh.trim.pick.names, group=2d.shhh.groups, start=1044, end=6332, processors=2)  
Pat