creating BAM? alignment files for IGV
Hi, I have coordinate data for several sequences I want to align against genomes in IGV. The preferred format for alignment is said to be BAM. Unfortunately I haven't found a straightforward way of creating BAMs straight from coordinates. I assume I'll need the reference genome as well. Is there any simple way to do it from R/Bioconductor?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Make genes from GTF annotation searchable in IGV
written by bataloffv •
-
Gene alignment with IGV
written by flappix •
-
Converting Bisulfite-seq BAM files to fastq
written by divyswar01 •
-
Is there a way to separate highly similar strains from metatranscriptomic data using HISAT2?
written by sheinsch •
-
BED alignments not positioned properly in IGV
written by bn •
-
[Solved] Problems merging TopHat mapped and unmapped BAMs for submission to ENA
written by Chris Cole
-
.bam file of human reference genome (hg19)
written by Max
-
For a given set of coordinates is there a simple fast way of determining the 'summit' coordinate,
written by User 9088 •
-
Convert Cds-Based Coordinate To Genomic Coordinates
written by Luca Beltrame
-
Tophat Junctions.Bed File
written by Varun Gupta
Do you have sequences you want to align, or do you have sequences (whose coordinates you know already) which you to display? If you have the genomic coordinates, all you need is a tab-delimited .BED file with:
And yes, to display on IGV you do need the reference genome.