fastq-dump

Question

[shersky]

I used fastq-dump to get an accession and it downloaded 4 files presumably I1, I2, and R1 and R2

but they are: SRR_1 SRR_2 SRR_3 SRR_4

I am not familiar with having four files.

Which one is R1 and which one is R2? How to know?

I modified the question to specify that they are single nuclei RNA sequencing:

head of each file:

Answer 1

[GenoMax]

I1 = SRR_1
I2 = SRR_2
R1 = SRR_3 (cell barcodes + UMI)
R2 = SRR_4 (RNA read)

[Ram]

Honestly, once demuxed, R1 and R2 files contain the I1 and I2 content thus making I1/I2 files unnecessary. Even the latest 10X flex protocol doesn't need the I1/I2 post demux.

Answer 2

[Mensur Dlakic]

It would help you to find out from SRR file description what exactly is present in the repository, as that will make it easier to understand. Beyond that, looking through file headers should also give an answer as paired-end reads will have the same headers. "Left" reads will likely have either :1 or /1 in their headers, while "right" reads will have either :2 or /2. Simply typing head file (where file should be replaced by an actual name) might give you enough information to match the reads.

[shersky]

i modified my question with an image. these are single nuclei RNA sequencing fastq files.

[Ram]

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