Sequence name does not match current genome - Tomato (ITAG 2.3)

[niranjan.s...@gmail.com]

Hi the IGV browser supports the latest Tomato (ITAG 2.3) version.
I downloaded the latest Tomato fasta file and used it for Variant calling with my sample.

What do I do if the BAM file I created contains many extra headers that cant be matched to the 12 chromiosome headers I see in the IGV file?

I saw this post:
The BAM file you're loading is expected to have chromosome names which match those in the genome file. You can workaround this by creating an alias file, see the bottom of http://www.broadinstitute.org/software/igv/LoadData

But my problem is that I have too many entires and niot just the 12 expected for the corresponding 12 chromosomes

An excerpt from the extracted headers -

...
...
...
@SQ    SN:SL2.40sc06977    LN:79909
@SQ    SN:SL2.40sc06883    LN:88651
@SQ    SN:SL2.40sc06638    LN:89525
@SQ    SN:SL2.40sc06380    LN:98720
@SQ    SN:SL2.40sc05016    LN:101297
@SQ    SN:SL2.40sc05417    LN:103173
@SQ    SN:SL2.40sc06557    LN:108142
@SQ    SN:SL2.40sc06569    LN:143262
@SQ    SN:SL2.40sc03959    LN:181585
@SQ    SN:SL2.40sc03714    LN:200883
@SQ    SN:SL2.40sc05190    LN:203142
@SQ    SN:SL2.40sc06206    LN:285891
@SQ    SN:SL2.40sc06388    LN:288687
@SQ    SN:SL2.40sc05241    LN:337182
@SQ    SN:SL2.40sc04463    LN:561203
@SQ    SN:SL2.40sc05224    LN:797762
@SQ    SN:SL2.40sc06396    LN:1579335
@SQ    SN:SL2.40sc04025    LN:1965685
@SQ    SN:SL2.40sc05082    LN:2191949
@SQ    SN:6    LN:49751636
@SQ    SN:2    LN:55340444
@SQ    SN:11    LN:56302525
@SQ    SN:10    LN:65527505
@SQ    SN:8    LN:65866657
@SQ    SN:5    LN:65875088
@SQ    SN:4    LN:66470942
@SQ    SN:12    LN:67145203
@SQ    SN:7    LN:68045021
@SQ    SN:3    LN:70787664
@SQ    SN:9    LN:72482091
@SQ    SN:1    LN:98543444
@RG    ID:D3NG5HQ1    LB:346    PL:Illumina    SM:VF36    PU:HN3VMADXX

[Jim Robinson]

Hi,

If you want to see alignments on those sequences, the best thing to do would be to download the fasta the BAM was aligned to then load it as a custom genome.

Jim

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[Niranjan Shirgaonkar]

Thank you Jim

I encountered a problem doing this before.

SInce I already had the fasta file, I created a .genome file from that fasta by specifying some ID and a descriptive name. After doing this, IGV creates a .genome file and the software pops up a window saying 'Defining Genome' and then does nothing.

My current PC has well over 1TB RAM and sufficient memory and yet the process was not completed even keeping it overnight. The bottom right corner of the screen was slowly showing increments like 110M of 1613M etc and increasing...

Sorry for the descriptive post but I dont have an idea about what is going wrong.

Regards,

Niranjan Shirgaonkar

Research Fellow, Indian Institute of Vegetable Research
email: niranjan.s...@gmail.com

skype: niranjanshirgaonkar

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[Jim Robinson]

Don't bother making the .genome file, just load the fasta.   It will have to index it first (create a .fai) file, this will happen automatically but might take some time.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CAD90L-pR8k8wCTVBEv98UO7xCi%3DaBhe4tiEr9mt2b84U2nS3gQ%40mail.gmail.com.

[Jim Robinson]

I meant to say load the fasta from the "Genomes" menu  (Load Genome from File),  not the "File" menu.

On 2/23/16 10:36 PM, Niranjan Shirgaonkar wrote:

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CAD90L-pR8k8wCTVBEv98UO7xCi%3DaBhe4tiEr9mt2b84U2nS3gQ%40mail.gmail.com.

[Niranjan Shirgaonkar]

Thanks a lot Jim. That solved my issue!

Regards,

Niranjan Shirgaonkar

Research Fellow, Indian Institute of Vegetable Research
email: niranjan.s...@gmail.com

skype: niranjanshirgaonkar

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/56CDC755.1050501%40broadinstitute.org.