2nd-seq data

[wyq977]

Hi I would like to reproduce some of the results from Raw data, however, I could not get the 2nd-seq data from the example dataset

I only found the fastq files for 1st-seq on https://deepblue.lib.umich.edu/data/concern/data_sets/9c67wn05f

DraI-100pM-mbcore-RD2.fastq.gz
>>> 1st-Seq raw MiSeq FASTQ output file for liver dataset
DraI_100pM_RD4.fastq.gz
>>> 1st-Seq raw MiSeq FASTQ output file for colon dataset

The GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169706) only provide

1) High definition map coordinate identifier (HDMI) sequence, tile and spatial coordinate information from 1st-Seq, (2) HDMI sequence, coupled with cDNA sequence from 2nd-Seq,

Can you clarify on where the raw data for 2nd-seq is located and how to access?

Best

[leeju-umich]

It is in the GEO. Thanks!

GSM5212842 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5212842 Liver_SeqScope_1st GSM5212843 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5212843 Colon_SeqScope_1st GSM5212844 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5212844 Liver_SeqScope_2nd GSM5212845 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5212845 Colon_SeqScope_2nd

On Fri, Dec 9, 2022 at 9:36 AM wyq977 @.***> wrote:

Hi I would like to reproduce some of the results from Raw data, however, I could not get the 2nd-seq data from the example dataset

I only found the fastq files for 1st-seq on https://deepblue.lib.umich.edu/data/concern/data_sets/9c67wn05f

DraI-100pM-mbcore-RD2.fastq.gz

1st-Seq raw MiSeq FASTQ output file for liver dataset DraI_100pM_RD4.fastq.gz 1st-Seq raw MiSeq FASTQ output file for colon dataset

The GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169706) only provide

1. High definition map coordinate identifier (HDMI) sequence, tile and spatial coordinate information from 1st-Seq, (2) HDMI sequence, coupled with cDNA sequence from 2nd-Seq,

Can you clarify on where the raw data for 2nd-seq is located and how to access?

Best

— Reply to this email directly, view it on GitHub https://github.com/leeju-umich/Cho_Xi_Seqscope/issues/13, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQLZFMNVQKNUBQAITQ5Z53TWMM7VFANCNFSM6AAAAAASZNIMOE . You are receiving this because you are subscribed to this thread.Message ID: @.***>

--

Jun Hee Lee, Ph.D. Professor of Molecular and Integrative Physiology Research Professor of Gerontology University of Michigan Medical School https://lee.lab.medicine.umich.edu/

[wyq977]

Thx!

[wyq977]

Hi just another question.

There're 7 runs in the 2nd-seq for liver data: https://www.ncbi.nlm.nih.gov/sra?term=SRX10457008.

Are these due to

multiple read alignments were performed using 25%, 50% and 75% subsets of the 2nd-Seq result

Which runs should I proceed with?

Best regards.

[leeju-umich]

I suggest you combine them and run everything. They are multiple sequencing runs of the same library.

All the best, Jun Hee

On Fri, Dec 9, 2022 at 10:13 AM wyq977 @.***> wrote:

Hi just another question.

There're 7 runs in the 2nd-seq for liver data: https://www.ncbi.nlm.nih.gov/sra?term=SRX10457008.

Are these due to

multiple read alignments were performed using 25%, 50% and 75% subsets of the 2nd-Seq result

Which runs should I proceed with?

Best regards.

— Reply to this email directly, view it on GitHub https://github.com/leeju-umich/Cho_Xi_Seqscope/issues/13#issuecomment-1344427160, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQLZFML7SSOTWY6DUNRGXWTWMNEB7ANCNFSM6AAAAAASZNIMOE . You are receiving this because you commented.Message ID: @.***>

--

Jun Hee Lee, Ph.D. Professor of Molecular and Integrative Physiology Research Professor of Gerontology University of Michigan Medical School https://lee.lab.medicine.umich.edu/