bayesembler

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Feature Request : Hisat2

1

Hi Lasse, This is similar to the request for STAR alignment support in bayesassembler. Is there anyway to give the program, HISAT2 alignments instead of Tophat2. Hisat2 as you know...

sanyalab

Insufficient number of observations

1

Can you please suggest what values should be manually assigned for resolving the following error? > [17/10/2017 11:26:33] Sorting splice-graphs by read count > [17/10/2017 11:26:33] Finished sorting splice-graphs by...

srbehera11

core dump when removing duplicates

2

Hi, I am trying to run Bayesembler on a tophat2 (2.0.8) generated file from human K562 whole cell polya+ RNAseq (dUTP protocol): https://www.encodeproject.org/files/ENCFF412EYU/@@download/ENCFF412EYU.bam Here is the command I ran on...

sdjebali

Error running bayesembler 1.2.0

4

When trying to run bayesembler 1.2.0 on an alignment generated by tophat2, I get the following error: bayesembler: /seqdata/krogh/jola/projects/transcriptome_assembly/code/release/bayesembler_1_2_0/src/assembler.cpp:186: void Assembler::markDuplicates(BamTools::BamAlignment&, Assembler::FirstReads_, Assembler::ReadPairs_): Assertion `cur_pos_first_reads_it->second.insert(pair(ri, new BamTools::BamAlignment(current_alignment))).second' failed. I assumed...

voshalla

error running bayesembler 1.2.0

8

I downloaded bayesembler 1.2.0 binary for linux, and run it on one of tophat2 generated bam files as follow: bayesembler -b ~/work/ngs_dat/project1/tophat2/sample1/accepted_hits.bam -o test But got following error: You are...

bosmont

bayesembler running errors

8

Recently, we use bayesembler to assemble transcriptome. We found 2 errors. First, the samtools in dependencies folder can not work well, but rebuild samtools can work well. Second bayesembler: /seqdata/krogh/jola/projects/transcriptome_assembly/code/release/bayesembler_1_1_1_pub_release/src/assembler.cpp:894:...

lmdu

CIGAR String error

7

Hello, I am trying to run bayesembler on a bam generated by GSNAP and have run into a CIGAR string error as below: bayesembler -s first -b ../GsnapAlignments/Gsnap.T1990_ctx.33080.cmu059.19.Aug.2014/T1990_ctx.all.mm.rg.dup.srtd.bam You are...

ashokrags

Error in Bayesembler v1.2.0

2

Hi, I'm trying to test Bayesembler, but so far with no successful results. My data is paired-end and I did run Tophat2 with default parameters. Still I'm getting error messages...

jpkoskin