10X dataset after snaptools dex-fastq

[znavidi]

Hi, In the "How to create snap file from 10X dataset" section, it is mentioned that we should run snaptools dex-fastq module to integrate the 10X barcode into the read name, and the output names are: Library1_1_L001_R1_001.dex.fastq.gz Library1_1_L001_R3_001.dex.fastq.gz Library1_2_L001_R1_001.dex.fastq.gz Library1_2_L001_R3_001.dex.fastq.gz

but you also mentioned that run the rest of the pipeline using Library1_L001_R1_001.fastq.dex.gz and Library1_L001_R3_001.fastq.dex.gz. The extension of the output of previous step and the files that you mentioned we should use for the rest of the pipeline is different (.dex.fastq.gz and .fastq.dex.gz). Is it a mistake in the names? Otherwise what do you mean and where are these files?

Thanks

[r3fang]

It’s a mistake

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On May 27, 2019, at 3:53 PM, znavidi notifications@github.com wrote:

Hi, In the "How to create snap file from 10X dataset" section, it is mentioned that we should run snaptools dex-fastq module to integrate the 10X barcode into the read name, and the output names are: Library1_1_L001_R1_001.dex.fastq.gz Library1_1_L001_R3_001.dex.fastq.gz Library1_2_L001_R1_001.dex.fastq.gz Library1_2_L001_R3_001.dex.fastq.gz

but you also mentioned that run the rest of the pipeline using Library1_L001_R1_001.fastq.dex.gz and Library1_L001_R3_001.fastq.dex.gz. The extension of the output of previous step and the files that you mentioned we should use for the rest of the pipeline is different (.dex.fastq.gz and .fastq.dex.gz). Is it a mistake in the names? Otherwise what do you mean and where are these files?

Thanks

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[r3fang]

Will correct it, thanks for reporting it

Sent from my iPhone

On May 27, 2019, at 3:53 PM, znavidi notifications@github.com wrote:

Hi, In the "How to create snap file from 10X dataset" section, it is mentioned that we should run snaptools dex-fastq module to integrate the 10X barcode into the read name, and the output names are: Library1_1_L001_R1_001.dex.fastq.gz Library1_1_L001_R3_001.dex.fastq.gz Library1_2_L001_R1_001.dex.fastq.gz Library1_2_L001_R3_001.dex.fastq.gz

but you also mentioned that run the rest of the pipeline using Library1_L001_R1_001.fastq.dex.gz and Library1_L001_R3_001.fastq.dex.gz. The extension of the output of previous step and the files that you mentioned we should use for the rest of the pipeline is different (.dex.fastq.gz and .fastq.dex.gz). Is it a mistake in the names? Otherwise what do you mean and where are these files?

Thanks

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[znavidi]

Thank you :) Also, after running dex-fastq command and integrating the barcode into the read name, it is mentioned to combine these two libraries (I think it means any number of different libraries):

$ cat Library1_1_L001_R1_001.fastq.gz Library1_2_L001_R1_001.fastq.gz > Library1_L001_R1_001.fastq.gz $ cat Library1_1_L001_R3_001.fastq.gz Library1_2_L001_R3_001.fastq.gz > Library1_L001_R3_001.fastq.gz

but the files that I have are from the different lanes (not library, because the only difference they have is in their L001, L002, L003 parts). So I should not combine them, right? I mean should I run the rest of the pipeline on each of the lane files separately?

[r3fang]

Hi there,

If it is the same library (same sample/experiment) just sequenced by different lanes, you should merge them. If it is different libraries, you should not merge them.

The demo example is different lanes from the same lib.

Sent from my iPhone

On May 27, 2019, at 4:03 PM, znavidi notifications@github.com wrote:

Thank you :) Also, after running dex-fastq command and integrating the barcode into the read name, it is mentioned to combine these two libraries (I think it means any number of different libraries):

$ cat Library1_1_L001_R1_001.fastq.gz Library1_2_L001_R1_001.fastq.gz > Library1_L001_R1_001.fastq.gz $ cat Library1_1_L001_R3_001.fastq.gz Library1_2_L001_R3_001.fastq.gz > Library1_L001_R3_001.fastq.gz

but the files that I have are from the different lanes (not library, because the only difference they have is in their L001, L002, L003 parts). So I should not combine them, right? I mean should I run the rest of the pipeline on each of the lane files separately?

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[znavidi]

Thanks

[znavidi]

Another question: By that sentence you mean we should merge Library-L001.dex.fastq.gz and Library-L002.dex.fastq.gz and ... together and align these Library-R1.dex.fastq.gz and Library-R2.dex.fastq.gz files to the reference genome?

[r3fang]

Yes

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On May 27, 2019, at 5:27 PM, znavidi notifications@github.com wrote:

Another question: By that sentence you mean we should merge Library-L001.dex.fastq.gz and Library-L002.dex.fastq.gz and ... together and align these Library-R1.dex.fastq.gz and Library-R2.dex.fastq.gz files to the reference genome?

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[r3fang]

i'll close this issue but feel free to ask any other question

[t-and]

Hi there @r3fang, thank you for putting this package together! Quick question that I think is pertinent to @znavidi 's question above -- at the end of the tutorial for making a snap file from 10X output, you write:

# combine these two library
$ cat Library1_1_L001_R1_001.fastq.gz Library1_2_L001_R1_001.fastq.gz > Library1_L001_R1_001.fastq.gz
$ cat Library1_1_L001_R3_001.fastq.gz Library1_2_L001_R3_001.fastq.gz > Library1_L001_R3_001.fastq.gz

Is this a typo to combine the fastq.gz files and not the demultiplexed dex.fastq.gz files?

Thanks!