"dual" option to include reads mapped to coding genes in TE quantification

[ss6025]

Dear author,

Thanks for making this fantastic tool. I am wondering where and how should I specify the parameter for "dual" option in the following command. No example is specified in the -help page.

SoloTE_pipeline.py --threads 8 --bam ${BAM_PATH}"/"${bam}"/count/sample_alignments.bam" --teannotation ${TE_BED} --outputprefix ${prefix} --outputdir ${bam}

Thanks, Siyu

[bvaldebenitom]

Hi @ss6025 !

This option was missing in the latest release. We fixed this for release 1.07, available here.

You can activate the "Dual" mode by adding the --dual flag to the command. An example using your command is as follows: SoloTE_pipeline.py --dual --threads 8 --bam ${BAM_PATH}"/"${bam}"/count/sample_alignments.bam" --teannotation ${TE_BED} --outputprefix ${prefix} --outputdir ${bam}

You should see the following message if the option is activated: Dual mode enabled. SoloTE will calculate TE expression also considering reads annotated to genes.

Please let me know if you find any issues!

[ss6025]

Thank you so much for the update!

On Mon, Apr 10, 2023 at 10:28 AM bvaldebenitom @.***> wrote:

Hi @ss6025 https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ss6025&d=DwMCaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=OEFxsYejLcXXsIYPNDdsGA&m=BQ5uHhNKZfceTGE_wnBbM_GiLHaE8Hg2iVFWuIot9ABlRawlllCRrQ7rPG3hLW0g&s=R4ZDE1A-nkDj92E5oESx0NJEWaQ4aYuhhXJA-Cz5dnM&e= !

This option was missing in the latest release. We fixed this for release 1.07, available here https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bvaldebenitom_SoloTE_releases_tag_1.07&d=DwMCaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=OEFxsYejLcXXsIYPNDdsGA&m=BQ5uHhNKZfceTGE_wnBbM_GiLHaE8Hg2iVFWuIot9ABlRawlllCRrQ7rPG3hLW0g&s=Y5rbACmg--I47BrbCccOFA-WGdiOGdgkpHmRJIZ74X8&e= .

You can activate the "Dual" mode by adding the --dual flag to the command. An example using your command is as follows: SoloTE_pipeline.py --dual --threads 8 --bam ${BAM_PATH}"/"${bam}"/count/sample_alignments.bam" --teannotation ${TE_BED} --outputprefix ${prefix} --outputdir ${bam}

You should see the following message if the option is activated: Dual mode enabled. SoloTE will calculate TE expression also considering reads annotated to genes.

Please let me know if you find any issues!

— Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bvaldebenitom_SoloTE_issues_13-23issuecomment-2D1501886188&d=DwMCaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=OEFxsYejLcXXsIYPNDdsGA&m=BQ5uHhNKZfceTGE_wnBbM_GiLHaE8Hg2iVFWuIot9ABlRawlllCRrQ7rPG3hLW0g&s=sef3Xi_zXRA8TqSpCWVp6b42NahQZAeHLKqZajn47Mw&e=, or unsubscribe https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ACEMTK2GCAIKCE3NTN3T2KLXAQKKPANCNFSM6AAAAAAWWZE5MU&d=DwMCaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=OEFxsYejLcXXsIYPNDdsGA&m=BQ5uHhNKZfceTGE_wnBbM_GiLHaE8Hg2iVFWuIot9ABlRawlllCRrQ7rPG3hLW0g&s=aF5FIe4mDklStJNs8OLneXM9LQ_pB7ukF8znEWRc4Kk&e= . You are receiving this because you were mentioned.Message ID: @.***>

-- Siyu Sun | PhD trained in Gresham Lab https://greshamlab.bio.nyu.edu/ (NYU) Cell: 917-767-3644 Email: @.***

[bvaldebenitom]

@ss6025 You are welcome! Please reach out should you encounter any issue running SoloTE.