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WGLab / w4CSeq

web server of 4C-Seq data analysis pipeline
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"paired-end data " option in Enzyme-digestion based analysis #3

Closed zhaocheng3326 closed 7 years ago

zhaocheng3326 commented 7 years ago

In enzyme_config.r, there is an option of "file_in: path to the raw fastq file". However , in sonication_config.r, there are option of "file_in1: path to the paired end raw fastq files #1" and "file_in2: path to the paired end raw fastq files #2". Is it meaning that we can only use 4C_enzyme_cmdline.R to analysis single-end data and use 4C_sonication_cmdline.R for paired-end data ?

nuoyazhou2 commented 7 years ago

Yes. The tool analyzes single-end enzyme digestion based 4C-Seq data and paired-end sonication based 4C-Seq data.

On Wed, Sep 27, 2017 at 4:31 AM, zhaocheng3326 notifications@github.com wrote:

In enzyme_config.r, there is an option of "file_in: path to the raw fastq file". However , in sonication_config.r, there are option of "file_in1: path to the paired end raw fastq files #1 https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_WGLab_w4CSeq_issues_1&d=DwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=rmADQazHldllb-vF1IdPBw&m=h90CsIGC2KVrxvmV0p-N8BR6HDNRkcdvSdSdA-K8VQg&s=s4R_K0OcZfgUnCxBKPyrO9aYYg7agsz2AdHqDgJ6n6A&e=" and "file_in2: path to the paired end raw fastq files #2 https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_WGLab_w4CSeq_issues_2&d=DwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=rmADQazHldllb-vF1IdPBw&m=h90CsIGC2KVrxvmV0p-N8BR6HDNRkcdvSdSdA-K8VQg&s=yYWQkBhHir6AUlpvJTrfgFqtbWvZNHfzuagfS_u3sNM&e= ". Is it meaning that we can only use 4C_enzyme_cmdline.R to analysis single-end data and use 4C_sonication_cmdline.R for paired-end data ?

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zhaocheng3326 commented 7 years ago

If I have 4C-Seq data which is paired-end and also made by enzyme-digestion. Is it ok to use 4C_sonication_cmdline.R to analysis it ?

nuoyazhou2 commented 7 years ago

No. The current framework only supports analysis of single-end enzyme digestion based 4C-Seq data.

On Wed, Sep 27, 2017 at 6:35 PM, zhaocheng3326 notifications@github.com wrote:

If I have 4C-Seq data which is paired-end and also made by enzyme-digestion. Is it ok to use 4C_sonication_cmdline.R to analysis it ?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_WGLab_w4CSeq_issues_3-23issuecomment-2D332701859&d=DwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=rmADQazHldllb-vF1IdPBw&m=Cwhxrf18pSl6VBRzlg3zGA20OFIvcV23p1Q1cxnKgac&s=UX26pmy5bPZ_YIXkBFT0vmNsPvlY6HY2XN8jCs0OBvI&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AOhFixJQmilovBR-2Dz6LEb7-2Dki2VeP5qRks5smvfZgaJpZM4Plntk&d=DwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=rmADQazHldllb-vF1IdPBw&m=Cwhxrf18pSl6VBRzlg3zGA20OFIvcV23p1Q1cxnKgac&s=Pm5Jg2cIGkfN-SkuWlI7CTVK-PR6iOEVxcrfyWZI5DY&e= .