# No.of unique sequence decreased to 15% after chimera.uch **URL:** \ **Category:** Commands in mothur\ **Created:** [October 24, 2014, 4:33pm UTC](https://forum.mothur.org/t/no-of-unique-sequence-decreased-to-15-after-chimera-uch/2099 "2014-10-24T16:33:32Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![Kumari\_Richa](https://avatars.discourse-cdn.com/v4/letter/k/51bf81/32.png) [@Kumari\_Richa](https://forum.mothur.org/u/Kumari_Richa)\ **Post date:** [October 24, 2014, 4:33pm UTC](https://forum.mothur.org/t/no-of-unique-sequence-decreased-to-15-after-chimera-uch/2099/1 "2014-10-24T16:33:32Z")
Hello , 1. I used greengenes reference taxonomy and alignment file. After doing Chimera.uchime and remove.seqs, I lost 85% of my unique sequences. Why ? 2. Another question, why screen.seq did not work ? Below is the summary written. mothur \> align.seqs(fasta=stability.trim.contigs.trim.good.unique.fasta, reference=gg.refalign, flip=T) mothur \> summary.seqs(fasta=current) Start End NBases Ambigs Polymer NumSeqs Minimum: 5 2263 370 0 3 1 2.5%-tile: 9 2266 370 0 4 312 25%-tile: 9 2266 371 0 4 3119 Median: 9 2266 372 0 5 6237 75%-tile: 9 2266 373 0 5 9355 97.5%-tile: 9 2266 376 0 6 12161 Maximum: 13 2293 376 0 8 12472 Mean: 9.01379 2266.03 372.169 0 4.71208 # of Seqs: 12472 mothur \> screen.seqs(fasta=stability.trim.contigs.trim.good.unique.align, count=stability.trim.contigs.trim.good.count\_table, summary=stability.trim.contigs.trim.good.unique.summary, start=9, end=2266, maxhomop=8) It took 1 secs to screen 12472 sequences. mothur \> summary.seqs(fasta=current, count=current) Using 8 processors. Start End NBases Ambigs Polymer NumSeqs Minimum: 5 2266 370 0 3 1 2.5%-tile: 9 2266 370 0 4 3339 25%-tile: 9 2266 372 0 4 33387 Median: 9 2266 372 0 5 66774 75%-tile: 9 2266 373 0 5 100161 97.5%-tile: 9 2266 376 0 6 130209 Maximum: 9 2293 376 0 8 133547 Mean: 8.99997 2266 372.232 0 4.62525 # of unique seqs: 12400 total # of seqs: 133547 Looking forward for suggestion. ---
**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:** [October 24, 2014, 7:36pm UTC](https://forum.mothur.org/t/no-of-unique-sequence-decreased-to-15-after-chimera-uch/2099/2 "2014-10-24T19:36:40Z")
> 1. I used greengenes reference taxonomy and alignment file. After doing Chimera.uchime and remove.seqs, I lost 85% of my unique sequences. Why ? Because a lot of your unique reads were chimeras. What percentage of your total reads were discarded? > 1. Another question, why screen.seq did not work ? Below is the summary written. Looks like it worked, what am I missing? ---
**Author:** ![Kumari\_Richa](https://avatars.discourse-cdn.com/v4/letter/k/51bf81/32.png) [@Kumari\_Richa](https://forum.mothur.org/u/Kumari_Richa)\ **Post date:** [October 27, 2014, 10:19am UTC](https://forum.mothur.org/t/no-of-unique-sequence-decreased-to-15-after-chimera-uch/2099/3 "2014-10-27T10:19:09Z")
Hi Dr. Schloss, 1. I realised from your question (what is the percentage of my total reads discarded) that I did not loose most of the total sequences. I still have 98% of total sequences. This means only 2 % of the total sequence makes 85% of rubbish unique sequences :shock: … 2) I wanted to exclude sequnce below 5 (start) and above 2266 (end). but I can still see them in summary.seq. However I can see reduction in no. of sequences. Thank you ---
**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:** [October 28, 2014, 4:00pm UTC](https://forum.mothur.org/t/no-of-unique-sequence-decreased-to-15-after-chimera-uch/2099/4 "2014-10-28T16:00:56Z")
the start option removes sequences that start _after_ the start position and the end option removes those that end _before_ the end position.