Question: Obtaining exon-intron and intron-exon reads
0
gravatar for fadhil.abubaker
2.6 years ago by
fadhil.abubaker20 wrote:

We're interested in studying the number of reads that start at an exon and "spill" over into the subsequent intron or vice-versa.

We have aligned .bam files and annotation files for h38. What tools/software could we use to get the number of reads from the .bam file that span exon-intron / intron-exon junctions?

rna-seq next-gen • 920 views
ADD COMMENTlink modified 2.5 years ago by Biostar ♦♦ 20 • written 2.6 years ago by fadhil.abubaker20

We have aligned .bam files

how. Which tool ?

ADD REPLYlink written 2.6 years ago by Pierre Lindenbaum133k

We used STAR to get the alignments.

ADD REPLYlink written 2.6 years ago by fadhil.abubaker20

Past thread with answers from @Pierre and @Devon: Extracting Intron-Exon Reads from bam files

ADD REPLYlink written 2.6 years ago by GenoMax94k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1107 users visited in the last hour