reformatting problem about asap_to_kite HOT 11 CLOSED

1. do you mean dependencies? If you get fastq files that look of reasonable length, then yu are probably okay
2. by default we reverse complemented because the i5 (10x scATAC barcode) is reverse complemented in the next-seq and nova-seq chemistry; if you sequenced your protein libraries on a Hiseq or Miseq, you should throw this flag
3. right so the idea is that you use the output of this python script as input to kallisto... the output here is to 'trick' the data into looking like scRNA-seq rather than the 3 fastqs in scatac

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Thank you so much for your response!

We have used Nova for sequencing. Would you please help me with writing the format of the command, when I am using Nova?
Do you have experience about Nova and how to change the command when my sequences are from Nova?
I am not sure how to add or remove the reverse complementing part in the code. I appreciate your support.

Thank you,
Sara

Best,
Sara

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You should just be able to run the script with the default parameters without the reverse complement if you did Nova-seq-- just follow the tutorial in the readme

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Hello,

Thank you so much.
My fastq file names are:

ASAPSeq003_TSA_S1_L002_I1_001.fastq.gz
ASAPSeq003_TSA_S1_L002_R1_001.fastq.gz
ASAPSeq003_TSA_S1_L002_R2_001.fastq.gz
ASAPSeq003_TSA_S1_L002_R3_001.fastq.gz
ASAPSeq003_TSB_S1_L002_I1_001.fastq.gz
ASAPSeq003_TSB_S1_L002_R1_001.fastq.gz
ASAPSeq003_TSB_S1_L002_R2_001.fastq.gz
ASAPSeq003_TSB_S1_L002_R3_001.fastq.gz

So I have TSA and TSB. But I am not sure how I should change to command to generate the correct output file. Can I ask your help to provide me the correct command?

Thank you,
Sara

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Sorry, about my previous message I wanted to add that all my barcodes (total TSA and TSB) are in one file (attached)

asapseq003_barcodes.csv

I think I am missing something when running the code, since my output results from kallisto has only few rows.

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Run these two commands:

python asap_to_kite_v2.py -f FASTQ_FOLDER -s ASAPSeq003_TSA -o TSA_PROCESSED -j TotalSeqA

python asap_to_kite_v2.py -f FASTQ_FOLDER -s ASAPSeq003_TSB -o TSB_PROCESSED -j TotalSeqB

Then take the PROCESSED R1 and R2 files and run them through kallisto with your barcode index

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from asap_to_kite.

Thank you so much!

Best,
Sara

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Thanks again for all your supports. I have a question about using my asap-to-kite fastq files for kallisto|bus.
I know that akllisto|bus is not your code, however I thought maybe you have some suggestions about my new questions:

1- do you know what is the correct format for the features.tsv file in the kallisto|bus tool?
For me, my output results of kallisto is generating:
adata.obs.head()
Empty DataFrame
Columns: []
Index: [AACCAACAGATGTTCC, AACCAACCAAAGGCCA, AACCAACCACGATTAC, AACCAACCATAGCCAT, AACCAACTCGCAGATT]

and my barcodes are appearing as the index. But I expect them to be a column not index.

Do you have any idea or tutorial about this feature barcode file?

Thank you

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I don't know for sure but my best guess is that it would follow this convention: https://github.com/pachterlab/kite

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