Mapping to a single Chromosome Tophat
I have a data set which relates to all the chromosomes which has been mapped to a whole genome using Tophat so this eventually produces mapped reads, but for all the chromosomes,
from these mapped reads output from tophat how do I obtain, the reads mapped to only one chromosome say chromomosome 1 only?
• 2,309 views
•
link
updated
by
Devon Ryan
•
written
by
benjyrolls
•
written
by
benjyrolls
2 answers
This has been asked and answered before, use samtools.
See e.g.,
How to generate a .sam/.bam file of a particular chromosome or even a particular region?
Since you used the Galaxy tag, I'll assume that you're doing this in Galaxy. In that case, you can use the "Filter SAM or BAM, output SAM or BAM" tool.
• 0 views
•
link
written
by
Devon Ryan
Log in to answer this question.
More posts like this
-
Using freebayes for variant calling, separate file for reference genome and expected mutations
written by sglass •
-
Calculating Average Coverage or Read Depth for a Sequence (WES)
written by Matt01 •
-
Uniquely mapped paired-end reads on the same chromosome
written by barzilayrom1 •
-
Is it possible to run bayescan with a splitted chromosome?
written by mataman_lib •
-
Reads mapping
written by Anst •
-
Amplicon sequencing and unwanted amplicons
written by misterie
-
Making reference fasta file from aligned sam file or bed file
written by vkgaur25 •
-
pindel somatic indel filter
written by Leandro de Mattos
-
Empty Cuffdiif Output except Gene Differential expression testing
written by benjyrolls
-
difference between tophat2 and bowtie2 alingner
written by zizigolu
