IGV 2.11.9 read alignment

[Huiping Chen]

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Dear Sir/Madam,

 

Below is the read alignment by IGV tool 2.11.9 using window computer. You can see very low coverage in the middle, in which the total count for a site is 13 (see below). But I do not see any aligned reads at that site. I wonder if some reads were not shown by the IGV tool? Thanks.

 

Best regards,

 

Chen Huiping, MD, PhD

University Hospital of Iceland

 

[igv-help]

I see from the black bar under the coverage that the alignments have been downsampled due to the deep coverage.   Downsampling is for the alignment display only, it does not effect the coverage count.     You can turn downsampling off or adjust parameters in the alignment preferences (select View > Preferences > Alignments tab).

[Huiping Chen]

Thanks. I use IGV 2.11.9. I wonder if it is too old? 

Best regards,

Chen

[James Robinson]

That is a fairly recent version.   In case I wasn't clear, your screenshot is normal and expected,  if coverage is very deep not all reads are displayed, only a representative sample, to prevent running out of memory.   You can turn this off in the IGV preferences.

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[Huiping Chen]

Many thanks. 

Attached is the read alignment by IGV, in which red reads, blue reads and grey reads can be seen. I wonder what the colors mean? Thanks.

Best regards,

Chen

[Huiping Chen]

Thanks. Attached is the description of reads. I wonder what the flags, pair orientation (F1R2 and F2R1), PG, NM, MQ, AS, XS, and hidden tags: MD mean? Many thanks for your help.

Best regards,

Chen

[igv-help]

Chen,

IGV has several options for coloring alignments via the track's right-click popup menu.
The default coloring mode for paired end reads is by "insert size and pair orientation". Pairs that have an unexpected insert size or unexpected pair orientation will have a color different from the default grey. Please see the section of the IGV documentation that describes viewing alignment data: https://software.broadinstitute.org/software/igv/AlignmentData. Regarding the description of the reads, IGV merely presents the read details from the BAM file. The specifics of what they mean is beyond the scope of this forum, but information about the BAM format can be found at http://samtools.github.io/hts-specs/. In particular, take a look at the SAM/BAM file format spec and the document describing tags.

Helga

[Huiping Chen]

Thanks, Helga.

Attached is read alignment (view as pairs), in which the third read pair from the top is marked by red, which means deletion in the insert. But I checked the two reads and found that just in the left alignment the read shows 70M6S, and the another read looks good. I wonder what kind of deletion happens in this insert? I also found that a pair of reads are marked by grey color, but the two reads have almost same condition: one read with 70M6S and another one normal.

For soft clipping and hard clipping, I wonder how to distinguish them? It seems that for both of them, the clipped parts are not shown in the read alignment. Thanks.

Best regards,

Chen

[Huiping Chen]

Thanks. Attached is read alignments in which very few reads are marked by red, blue, green etc.. I wonder if deletion (red), insertion (blue), inversion and tandem duplication really happened in the genome, or just artifacts or sequencing errors? Thanks.

Best regards,

Chen

[igv-help]

Chen,

You can enable the display of soft-clipped bases via View > Preferences > Alignments. IGV cannot display hard-clipped bases.

The presence of stray abnormal reads is unlikely to indicate actual variants.  With that said, please note that the analysis/interpretation of user data is beyond the scope of this forum.

Helga

[Huiping Chen]

Thanks. 

Attached is about reads alignment by IGV tool, in which the Bam junctions appear on the second track. I am wondering what the bam junctions mean? Can I remove it? Thanks.

Best regards,

Chen