Fastq manifest formats help

me again! I am attempting to do something different with my data as I did not make a manifest file first. I am having difficulty figuring out how to create the.csv as I find the tutorial online hard to understand. Where am I typing the names of these samples into? Do I go to excel to make the manifest ? Also what is each indicative of in the following?

sample-id,absolute-filepath,direction
# Lines starting with '#' are ignored and can be used to create
# "comments" or even "comment out" entries
sample-1,$PWD/some/filepath/sample1_R1.fastq.gz,forward
sample-2,$PWD/some/filepath/sample2_R1.fastq.gz,forward
sample-1,$PWD/some/filepath/sample1_R2.fastq.gz,reverse
sample-2,$PWD/some/filepath/sample2_R2.fastq.gz,reverse

Is there anyway I can get an example of what a manifest file should look like? Should I use keemei? If so how should I format the rows? Any help would be would be much appreciated, because I am lost.

(update) Additionally forgot to add the names of my fastq files:

Female-1-1_S13_L001_R1_001.fastq.gz

Female-1-1_S13_L001_R2_001.fastq.gz

Female-1-2_S14_L001_R1_001.fastq.gz

Female-1-2_S14_L001_R2_001.fastq.gz

Female-2-1_S15_L001_R1_001.fastq.gz

Female-2-1_S15_L001_R2_001.fastq.gz

Female-2-2_S16_L001_R1_001.fastq.gz

Female-2-2_S16_L001_R2_001.fastq.gz

Female-3-1_S17_L001_R1_001.fastq.gz

Female-3-1_S17_L001_R2_001.fastq.gz

Female-3-2_S18_L001_R1_001.fastq.gz

Female-3-2_S18_L001_R1_001.fastq.gz

Female-4-1_S19_L001_R1_001.fastq.gz

Female-4-1_S19_L001_R2_001.fastq.gz

Female-4-2_S20_L001_R1_001.fastq.gz

Female-4-2_S20_L001_R2_001.fastq.gz

Female-5-1_S21_L001_R1_001.fastq.gz

Female-5-1_S21_L001_R2_001.fastq.gz

Female-5-2_S22_L001_R1_001.fastq.gz

Female-5-2_S22_L001_R2_001.fastq.gz

Female-6-1_S23_L001_R1_001.fastq.gz

Female-6-1_S23_L001_R2_001.fastq.gz

Female-6-2_S24_L001_R1_001.fastq.gz

Female-6-2_S24_L001_R2_001.fastq.gz

Male-1-1_S1_L001_R1_001.fastq.gz

Male-1-1_S1_L001_R2_001.fastq.gz

Male-1-2_S2_L001_R1_001.fastq.gz

Male-1-2_S2_L001_R2_001.fastq.gz

Male-2-1_S3_L001_R1_001.fastq.gz

Male-2-1_S3_L001_R2_001.fastq.gz

Male-2-2_S4_L001_R1_001.fastq.gz

Male-2-2_S4_L001_R2_001.fastq.gz

Male-3-1_S5_L001_R1_001.fastq.gz

Male-3-1_S5_L001_R2_001.fastq.gz

Male-3-2_S6_L001_R1_001.fastq.gz

Male-3-2_S6_L001_R1_001.fastq.gz

Male-4-1_S7_L001_R1_001.fastq.gz

Male-4-1_S7_L001_R2_001.fastq.gz

Male-4-2_S8_L001_R1_001.fastq.gz

Male-4-2_S8_L001_R2_001.fastq.gz

Male-5-1_S9_L001_R1_001.fastq.gz

Male-5-1_S9_L001_R2_001.fastq.gz

Male-5-2_S10_L001_R1_001.fastq.gz

Male-5-2_S10_L001_R2_001.fastq.gz

Male-6-1_S11_L001_R1_001.fastq.gz

Male-6-1_S11_L001_R2_001.fastq.gz

Male-6-2_S12_L001_R1_001.fastq.gz

Male-6-2_S12_L001_R2_001.fastq.gz
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Hi there @desiree757!

Ideally a text editor or a spreadsheet program. I like to use Google sheets or Excel!

You pasted one just above! You could just open this in Excel and edit it to meet your needs.

Nope - that is for validating QIIME 2 Metadata --- your manifest is not Metadata, so no worries there!

:world_map: :heart: :qiime2:

Perfect - now add those names to your new manifest file, and indicate which sample they belong to, and the read direction! Feel free to post a snippet of your manifest file once you get started, we can lay our :eyes: on it for you.

Happy QIIMEing! :sunflower:

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@thermokarst once again you are amazing ! One quick question how would I edit the excel to meet my needs for the files I have? Like what should I name the columns if that makes sense? Is there anyway you could use one of mine to show me as an example?

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The column names are fixed β€” sample-id,absolute-filepath,direction

sample-id,absolute-filepath,direction
Female-1-1,/path/to/file/Female-1-1_S13_L001_R1_001.fastq.gz,forward
Female-1-1,/path/to/file/Female-1-1_S13_L001_R2_001.fastq.gz,reverse
Female-1-2,/path/to/file/Female-1-2_S14_L001_R1_001.fastq.gz,forward
Female-1-2,/path/to/file/Female-1-2_S14_L001_R2_001.fastq.gz,reverse
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thank you again! I will upload my manifest as soon as I type them out so I can make sure I have formatted the cells correctly!

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How do I save the excel as a .csv file and was I supposed to type it all in one line or separate columns like I did?

File -> Save As -> then check out the delimited options in there.

Looks good to me.

Please note though, the absolute-filepath column needs to have filepaths that point to your files β€” you appear to have copied my boilerplate text from above, you will need to update that with a real path to the file.

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27%20PM

Hi so if the files are in this folder do I say path/to/gartersnakereads ?
and then absolute-gartersnakereads ?

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Well, β€œpath/to” needs to be an actual place on your computer, right? So for example:

/Users/desiree757/qiime2-analysis/gartersnakereads/Female-1-1_S13_L001_R1_001.fastq.gz

No β€” the header is always the same:

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this is my path do I need to add the "/" before Users I just noticed yours!

Yep!

Otherwise, this is looking good to me!

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