# sffinfo trimming 1 extra good base

**URL:** <https://forum.mothur.org/t/sffinfo-trimming-1-extra-good-base/2411>\
**Category:** mothur bugs\
**Created:** [June 19, 2015, 5:47pm UTC](https://forum.mothur.org/t/sffinfo-trimming-1-extra-good-base/2411 "2015-06-19T17:47:13Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![miked](https://avatars.discourse-cdn.com/v4/letter/m/ed655f/32.png) [@miked](https://forum.mothur.org/u/miked)\
**Post date:** [June 19, 2015, 5:47pm UTC](https://forum.mothur.org/t/sffinfo-trimming-1-extra-good-base/2411/1 "2015-06-19T17:47:13Z")

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Hello,

I’m using sffinfo within mothur as follows:

mothur -q “#sffinfo(sff=454Reads.RL6.sff, flow=F);”

I get the FASTA & QUAL files as expected. What I’ve noticed is that an extra base ( one more than what is indicated in “Clip Qual Right:” ) is trimmed off. Looks like it may be an off-by-one bug here. A visual look at the soft masked bases within the SFF file can confirm this as well.

With regards to “Clip Qual Right:” , this is not how sffinfo from 454tools or process\_sff.py from QIIME is functioning during SFF to FASTA conversion.

Can you confirm this behavior on your end? Am I missing something obvious? I will admit I’m a new user to mothur and how SFF files are processed.

Let me know if you require me to provide some examples.

Thanks for your support on this.

Mike

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**Author:** ![miked](https://avatars.discourse-cdn.com/v4/letter/m/ed655f/32.png) [@miked](https://forum.mothur.org/u/miked)\
**Post date:** [June 19, 2015, 8:29pm UTC](https://forum.mothur.org/t/sffinfo-trimming-1-extra-good-base/2411/2 "2015-06-19T20:29:33Z")

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I wanted to add that I’m using version:

mothur v.1.35.1  
Last updated: 03/31/2015

Another question: does sffinfo always read ‘Clip Qual Left:’ to be 5 ?

Thanks

Mike

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**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [July 1, 2015, 5:52pm UTC](https://forum.mothur.org/t/sffinfo-trimming-1-extra-good-base/2411/3 "2015-07-01T17:52:49Z")

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Thanks for reporting this bug Mike. I have fixed the issue and the change will be part of our next release 1.36.0.