how to obtain read names / co-ordinates to inspect on IGV

[proukakis]

Hello, this is great, and apologies if i am missing something obvious. I have CNV calls based on single cell low coverage WGS, with boundaries very imprecise, and trying to find support in bulk Illumina 85x data. eg this is a nice one- but i really want to look at the reads on IGV- could you explain how to get them?. thanks

[proukakis]

hi, would love some info if possible before we finalise preprint, thanks

[jbelyeu]

This issue is a bit out of scope, relating perhaps more to IGV than to samplot SV review. However, you could clone/fork this repository and add a print statement in the plot function - after the get_read_data() call, to print out the read_data dictionary. Should output the read names that are included in the plot.

[proukakis]

Ok that sounds great, thanks From: Jon Belyeu ***@***.***> Reply to: ryanlayer/samplot ***@***.***> Date: Thursday, 3 August 2023 at 23:55 To: ryanlayer/samplot ***@***.***> Cc: "Proukakis, Christos" ***@***.***>, Author ***@***.***> Subject: Re: [ryanlayer/samplot] how to obtain read names / co-ordinates to inspect on IGV (Issue #185) ⚠ Caution: External sender This issue is a bit out of scope, relating perhaps more to IGV than to samplot SV review. However, you could clone/fork this repository and add a print statement in the plot function - after the get_read_data() call, to print out the read_data dictionary. Should output the read names that are included in the plot. — Reply to this email directly, view it on GitHub<#185 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AENBYSCWLGIYXZSE6FDSNL3XTQT5VANCNFSM6AAAAAAZZ2IGTI>. You are receiving this because you authored the thread.Message ID: ***@***.***>