# Problem with fixing a -p-trim-left and –p-trunc-len parameters due to the bad quality

**URL:** https://forum.qiime2.org/t/problem-with-fixing-a-p-trim-left-and-p-trunc-len-parameters-due-to-the-bad-quality/5572
**Category:** User Support
**Created:** [August 14, 2018, 12:16pm UTC](https://forum.qiime2.org/t/problem-with-fixing-a-p-trim-left-and-p-trunc-len-parameters-due-to-the-bad-quality/5572 "2018-08-14T12:16:51Z")
**Posts on this page:** 5
**Page:** 1

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### Author: ![Hajar](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/h/d9b06d/32.png) [@Hajar](https://forum.qiime2.org/u/Hajar)
#### Post date: [August 14, 2018, 12:16pm UTC](https://forum.qiime2.org/t/problem-with-fixing-a-p-trim-left-and-p-trunc-len-parameters-due-to-the-bad-quality/5572/1 "2018-08-14T12:16:51Z")

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Hi,  
I would like to give a brief summary of what I want to do:  
I received 3 files from the company: \_bcSorted.tar.gz, \_trimmed.tar.gz, \_joined.tar.gz.

I used\_joined.tar.gz after unzipping, I picked the fastq.gz files ending with un1- and un2 only and deleted the files ending with joined.fastq.gz.  
I prepared the manifest file using Paired end read type, and it was successfully imported. However when I want to move on to the denoising step, I got this quality please see below.

I am now unable to choose --p-trim-left and  
--p-trunc-len. Because of the low quality observed.  
Do you have any suggestions why the quality is bad Is that because I choose the wrong file?

 ![IMG_2150](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/6/6871ec496f7bc4c9d7683f966f52da2ad3603df8.jpeg) ![IMG_2149](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/3/3fe83f22d2265b286c482313499e81cff0a3d28e.jpeg) ![IMG_2148](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/b/b36af7d451381f0d64128f20d357d8cea9270fb5.jpeg)

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### Author: ![ebolyen](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ebolyen/32/11_2.png) [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [August 14, 2018, 5:44pm UTC](https://forum.qiime2.org/t/problem-with-fixing-a-p-trim-left-and-p-trunc-len-parameters-due-to-the-bad-quality/5572/2 "2018-08-14T17:44:05Z")

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### Author: ![ebolyen](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ebolyen/32/11_2.png) [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [August 16, 2018, 7:36pm UTC](https://forum.qiime2.org/t/problem-with-fixing-a-p-trim-left-and-p-trunc-len-parameters-due-to-the-bad-quality/5572/3 "2018-08-16T19:36:05Z")

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Hey @Hajar!

Those pictures don't look awesome for quality scores, I would agree. I don't think I have a recommendation here either, but it does look like some processing has already been done as a lot of your reads are shorter than the rest. I assume `_joined.targ.gz` came after `_trimmed.tar.gz` in their pipeline.

What is inside of `_bcSorted.tar.gz`, I could see that file-name potentially representing "demultiplexed", so it might have your "raw-er" data.

If so, I would try working from that instead, it probably won't help with the quality scores, but I would see what DADA2 is able to do with a few different trim-points.

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### Author: ![ebolyen](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ebolyen/32/11_2.png) [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [August 16, 2018, 7:36pm UTC](https://forum.qiime2.org/t/problem-with-fixing-a-p-trim-left-and-p-trunc-len-parameters-due-to-the-bad-quality/5572/4 "2018-08-16T19:36:28Z")

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### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [September 17, 2018, 1:36am UTC](https://forum.qiime2.org/t/problem-with-fixing-a-p-trim-left-and-p-trunc-len-parameters-due-to-the-bad-quality/5572/5 "2018-09-17T01:36:29Z")

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