# using a manifest file to import data or just instruct what the forward and reverse file is

**URL:** https://forum.qiime2.org/t/using-a-manifest-file-to-import-data-or-just-instruct-what-the-forward-and-reverse-file-is/27889
**Category:** Ideas and Suggestions
**Tags:** import
**Created:** [October 9, 2023, 12:31pm UTC](https://forum.qiime2.org/t/using-a-manifest-file-to-import-data-or-just-instruct-what-the-forward-and-reverse-file-is/27889 "2023-10-09T12:31:41Z")
**Posts on this page:** 6
**Page:** 1

<div class="post-metadata">

### Author: ![fenny](https://forum.qiime2.org/user_avatar/forum.qiime2.org/fenny/32/21859_2.png) [@fenny](https://forum.qiime2.org/u/fenny)
#### Post date: [October 9, 2023, 12:31pm UTC](https://forum.qiime2.org/t/using-a-manifest-file-to-import-data-or-just-instruct-what-the-forward-and-reverse-file-is/27889/1 "2023-10-09T12:31:41Z")

</div>

Maybe I'm missing something, but when I am importing data before demuxing I always have to copy my original filenames to forward.fastq.gz and reverse.fastq.gz.

I sometimes have multiple files for a library and in that case it would be handy if one could use a manifest file to specify the files to load. One of the reasons would be easily exclude files with bad quality sequences

something like

```auto
qiime tools import --type MultiplexedPairedEndBarcodeInSequence --input-manifest ./manifest.tsv --output-path ./qiime_artifacts/xyz

```

where the manifest file would look something like

```auto
forward_reads reverse_reads
<path>/F123_1_1.fastq.gz <path>/F123_1_2.fastq.gz
<path>/F123_2_1.fastq.gz <path>/F123_2_2.fastq.gz
<path>/F123_3_1.fastq.gz <path>/F123_3_2.fastq.gz

```

---

<div class="post-metadata">

### Author: ![colinvwood](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinvwood/32/17303_2.png) [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [October 10, 2023, 5:10pm UTC](https://forum.qiime2.org/t/using-a-manifest-file-to-import-data-or-just-instruct-what-the-forward-and-reverse-file-is/27889/2 "2023-10-10T17:10:47Z")

</div>

Hello @fenny,

What do you do now instead when you have multiple multiplexed files?

---

<div class="post-metadata">

### Author: ![fenny](https://forum.qiime2.org/user_avatar/forum.qiime2.org/fenny/32/21859_2.png) [@fenny](https://forum.qiime2.org/u/fenny)
#### Post date: [October 18, 2023, 12:23pm UTC](https://forum.qiime2.org/t/using-a-manifest-file-to-import-data-or-just-instruct-what-the-forward-and-reverse-file-is/27889/3 "2023-10-18T12:23:43Z")

</div>

We currently have to concatenate all forward files and all reverse files before feeding them to the import.

For large projects it would be handy to have a manifest files with library code as well. E.g :

```auto
forward_reads reverse_reads libraryNumber
<path>/F123_1_1.fastq.gz <path>/F123_1_2.fastq.gz L1
<path>/F123_2_1.fastq.gz <path>/F123_2_2.fastq.gz L1
<path>/F123_3_1.fastq.gz <path>/F123_3_2.fastq.gz L2

```

As far as I'm aware, demuxing should be done on a 'per library' basis, given that barcodes might be shared among libraries. In the case below Sample\_1 and Sample\_3 will become mixed in the current setup.

Adding library awareness should be able to demux the samples correctly based on the file manifest data and the demultiplexing sample sheet if it contains the library number

```auto
#SampleID	forwardBarcodeSequence	reverseBarcodeSequence	LibraryNumber
Sample_1	AACCAGAA AACCAGAA L1
Sample_2	AACCATGC AACCATGC L1
Sample_3	AACCAGAA AACCAGAA L2
Sample_4	AACCATGC AACCATGC L2

```

A setup like this would facilitate automated analysis across many samples sequenced over a larger amount of time, in one go.

---

<div class="post-metadata">

### Author: ![lizgehret](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lizgehret/32/17128_2.png) [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [October 23, 2023, 5:15pm UTC](https://forum.qiime2.org/t/using-a-manifest-file-to-import-data-or-just-instruct-what-the-forward-and-reverse-file-is/27889/6 "2023-10-23T17:15:25Z")

</div>



---

<div class="post-metadata">

### Author: ![cherman2](https://forum.qiime2.org/user_avatar/forum.qiime2.org/cherman2/32/17129_2.png) [@cherman2](https://forum.qiime2.org/u/cherman2)
#### Post date: [October 23, 2023, 5:49pm UTC](https://forum.qiime2.org/t/using-a-manifest-file-to-import-data-or-just-instruct-what-the-forward-and-reverse-file-is/27889/8 "2023-10-23T17:49:42Z")

</div>



---

<div class="post-metadata">

### Author: ![cherman2](https://forum.qiime2.org/user_avatar/forum.qiime2.org/cherman2/32/17129_2.png) [@cherman2](https://forum.qiime2.org/u/cherman2)
#### Post date: [October 23, 2023, 6:02pm UTC](https://forum.qiime2.org/t/using-a-manifest-file-to-import-data-or-just-instruct-what-the-forward-and-reverse-file-is/27889/10 "2023-10-23T18:02:53Z")

</div>

Hi @fenny,  
Thanks for your great description!  
Would you mind opening up an issue on our github: [GitHub - qiime2/q2-metadata](https://github.com/qiime2/q2-metadata)? That way this will stay on our radar for when we have time to implement this.  
Thank you again!