clustering counts about leafcutter HOT 8 CLOSED

On Fri, Jun 2, 2017 at 11:10 PM, Stathis ***@***.***> wrote: Hello, I've re-aligned the Geuvadis RNA-Seq data using STAR. I've made junc files using leafcutter, as well as clustered all the data using two settings: -m10 and the default -m50. I'm trying to understand the numbers reported in perind.counts.gz using IGV. Here are the numbers: - for -m 10: 8/24 - for -m 50: 7/21 Here is a screenshot of the bam with the junction in question (20:270948-271056) highlighted in orange: [image: screen shot 2017-06-02 at 15 52 20] <https://cloud.githubusercontent.com/assets/1259045/26731989/e42979b8-47ad-11e7-8539-e499cd8d964e.png> Can you help me interpret these counts based on this picture? Thanks a lot. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#23>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE1piYQSghYVIwny8GF87D8CgtkEqRdaks5sACXzgaJpZM4NuaXX> .

On Mon, Jun 5, 2017 at 8:43 PM, Stathis ***@***.***> wrote: Hi Yang, 1. No but you can see them in the screenshot clearly. They are the blocks broken up by a line. 2. The count for this junction is 1 Thanks again — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#23 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE1piS1wDN4_zxdrMZQPH8NE-XkLslYgks5sA_fsgaJpZM4NuaXX> .

On Tue, Jun 6, 2017 at 5:42 PM, Stathis ***@***.***> wrote: - junc file (HG01789.bam.junc): 20 270948 271055 . 1 - - perind file (-m 50): 20:270948:271056:clu_3 0/0 0/0 7/21 0/0 0/5 ... - perind file (-m 10): 20:270948:271056:clu_3 0/0 0/0 8/24 0/0 0/6 ... - header: chrom HG00101.bam NA12347.bam *HG01789.bam* HG00174.bam NA19099.bam ... Thanks again! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#23 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE1piXV8NkAvk7Aq-6PKOAOz6lEGYZMeks5sBR8agaJpZM4NuaXX> .

On Tue, Jun 6, 2017 at 6:18 AM, Stathis ***@***.***> wrote: The bam is here: http://wwwdev.ebi.ac.uk/~natal ja/star_GRCh37.87/HG01789.bam I'm attaching the junc file: HG01789.bam.junc.txt <https://github.com/davidaknowles/leafcutter/files/1055127/HG01789.bam.junc.txt> — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#23 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE1piSby3bL9HbSdpuBu_fEpN_rDTmtwks5sBVGWgaJpZM4NuaXX> .