how to prepare the csv file for the count_spacers.py from miseq data?

[hylei]

Dear all:

We just got our miseq data. Can anyone please give me some suggestions about "Prepare a csv file containing the guide spacer sequences with each line corresponding to one sequence" before running count_spacers.py? Thanks very much.

best

HY

[Julia Joung]

Hi HY,

If you obtained the sgRNA library from Addgene, I would suggest downloading the sgRNA target sequence file from their website. This is usually an excel spreadsheet that you can edit to remove everything except for the sgRNA target sequences, and then save as a .csv file before running count_spacers.py.

Best,

Julia

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[LEI FANG]

Hi Julia or Hylei, 

Could you please send me the csv file cuz I couldn't download it from addgene website?  There is the link to download sgRNA target sequence, but it takes forever to load and never download.   Thanks in advance. 

Sincerely,

Elaine

On Wednesday, May 10, 2017 at 5:34:08 PM UTC-5, Julia Joung wrote:

Hi HY,

If you obtained the sgRNA library from Addgene, I would suggest downloading the sgRNA target sequence file from their website. This is usually an excel spreadsheet that you can edit to remove everything except for the sgRNA target sequences, and then save as a .csv file before running count_spacers.py.

Best,

Julia

On Wed, May 10, 2017 at 1:42 PM, hylei <lhai...@gmail.com> wrote:

Dear all:

We just got our miseq data. Can anyone please give me some suggestions about "Prepare a csv file containing the guide spacer sequences with each line corresponding to one sequence" before running count_spacers.py? Thanks very much.

best

HY

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[LEI FANG]

I called addgene customer service, and they asked me to contact Dr. Zhang lab directly.   They said the website has been down for a while.    Thanks.

Elaine

[Mark]

Lei, the Addgene link works properly. Download the ZIP, not the FASTQ.