Fastq manifest formats help

[desiree757 (Desiree)]

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

[thermokarst]

Hi there @desiree757!

@desiree757

Where am I typing the names of these samples into?

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

@desiree757

Is there anyway I can get an example of what a manifest file should look like?

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

@desiree757

Should I use keemei?

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

@desiree757

Any help would be would be much appreciated, because I am lost.

:qiime2:

@desiree757

Additionally forgot to add the names of my fastq files

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 on it for you.

Happy QIIMEing!

[desiree757 (Desiree)]

@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?

[thermokarst]

@desiree757

Like what should I name the columns if that makes sense?

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

@desiree757

Is there anyway you could use one of mine to show me as an example

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

[desiree757 (Desiree)]

@thermokarst

path/to/file/Female-1-1_S13_L001_R2_001.fastq.gz

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!

[desiree757 (Desiree)]

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?

[thermokarst]

@desiree757

How do I save the excel as a .csv file

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

@desiree757

was I supposed to type it all in one line or separate columns like I did?

Looks good to me.

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

[desiree757 (Desiree)]

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

[thermokarst]

@desiree757

do I say path/to/gartersnakereads

Well, "path/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

@desiree757

and then absolute-gartersnakereads

No --- the header is always the same:

@thermokarst

The column names are fixed — sample-id,absolute-filepath,direction

[desiree757 (Desiree)]

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

[thermokarst]

@desiree757

do I need to add the “/” before Users

Yep!

Otherwise, this is looking good to me!