Insertion and deletion call by IGV

[Huiping Chen]

Dear Sir/Madam,

Attached is my NGS data analysis by IGV (versin 2.11.9.12), in which 3 bases insertions and 3 bases deletions are shown clearly. However, the insertions and deletions are not shown in the consensus sequences when I copied consensus sequences from the IGV tool. I wonder how the consensus sequences could include the insertions and deletions identified? Thanks.

Best regards,

Chen Huiping, MD, PhD

University Hospital of Iceland

[igv-help]

Indels are not included in consensus sequence,  what IGV does is described below.

Calculates the consensus sequence for the region in view and copies the information to the clipboard. The method for calculating the consensus is taken from Cavener, Nucleic Acids Res. 15, 1353-1361, 1987.

1. If the frequency of a single nucleotide at a specific position is greater than 50% and greater than twice the number of the second most frequent nucleotide it is assigned as the consensus nucleotide.

2. If the sum of the frequencies of two nucleotides is greater than 75% (but neither meet the criteria for a single nucleotide assignment) they are assigned as co-consensus nucleotides.

3. If no single nucleotide or pair of nucleotides meets the criteria,  assign an 'N'.

Information copied to the clipboard includes:

• Locus of the copied sequence (i.e., region currently in view)
• The consensus sequence.
• A matrix with the details of all nucleotide counts used to calculate the consensue sequence. Rows in the matrix correspond to the bases along the sequence. The values in a row show the counts for each type of nucleotide at that locus. A header row above the matrix indicates the order of the nucleotide columns (A, C, G, T, and N).

[neha dinesh]

Hi ,

Can someone help me with two aspects regarding the sashimi plot.

1. What does it mean when some of the arcs are on top side versus when it is below. For example in the image 1 below, both red and blue samples have arcs on top while green one has arcs below.

2. For a complex gene splicing as image one in image 2, is there a way to modify the complexity by changing arc line thickness or so. Also is it normal to  see such a complex splicing pattern?

Thank you so much 

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/c401c0d5-81e0-4b53-b354-66692be0a951n%40googlegroups.com.

[neha dinesh]

To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+unsubscribe@googlegroups.com.

[James Robinson]

The arc placement above or below doesn't mean anything, its just a way of using space efficiently.    You can filter some of the splices out based on coverage with the "Set Junction Coverage Min" from the menu.    

[neha dinesh]

Ok thank you. 

Just to be sure I understand correctly, the part that the arcs connect are the regions spliced out ?

For example if I see an arc from exon 1 to exon 4 that means it indicates reads with exons 1 to 4 spliced out ?

Thank you in advance 

Neha 

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.

To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2BpunWOuo-jivrJzrRKHm6wX%3DZiMe4u1VRT2XxUraqaFitw%40mail.gmail.com.

[James Robinson]

It would mean that exons 2 and 3 are spliced out,  or in other words that exon 1 is spliced to exon 4.

On Wed, Nov 16, 2022 at 12:55 PM neha dinesh <neha...@gmail.com> wrote:

Ok thank you. 

Just to be sure I understand correctly, the part that the arcs connect are the regions spliced out ?

For example if I see an arc from exon 1 to exon 4 that means it indicates reads with exons 1 to 4 spliced out ?

Thank you in advance 

Neha 

On Wednesday, November 16, 2022, James Robinson <jrob...@broadinstitute.org> wrote:

The arc placement above or below doesn't mean anything, its just a way of using space efficiently.    You can filter some of the splices out based on coverage with the "Set Junction Coverage Min" from the menu.    

On Tue, Nov 15, 2022 at 2:01 PM neha dinesh <neha...@gmail.com> wrote:

Hi ,

Can someone help me with two aspects regarding the sashimi plot.

1. What does it mean when some of the arcs are on top side versus when it is below. For example in the image 1 below, both red and blue samples have arcs on top while green one has arcs below.

2. For a complex gene splicing as image one in image 2, is there a way to modify the complexity by changing arc line thickness or so. Also is it normal to  see such a complex splicing pattern?

Thank you so much 

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.

To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2BpunWOuo-jivrJzrRKHm6wX%3DZiMe4u1VRT2XxUraqaFitw%40mail.gmail.com.

--

---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/abJKWxo5mts/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CAA5%2B_vQHFiVQjdgak%3Dss7VWmaLykzGNb1XaNL0fr2_TqkU4k-Q%40mail.gmail.com.