-
```
What steps will reproduce the problem?
1. Start with an rna-seq bam file
2. Query a region that includes spliced reads overlaping a position using
pysam.pileup()
3. Try to get the allele frequenc…
-
Hi,
I'm trying to launch a stringTie assembly on a rather large BAM file (81G), and the call systematically ends with an 'error allocating memory'. I monitored it and saw that it used up to 128 GB of …
plger updated
8 years ago
-
Dear Tim,
I have a big stranded RNA-seq data set from human (10 conditions and 50 samples). I want to use Vast-tools and diff for differential alternative splicing analysis and estimation of intron r…
-
```
What steps will reproduce the problem?
1. Start with an rna-seq bam file
2. Query a region that includes spliced reads overlaping a position using
pysam.pileup()
3. Try to get the allele frequenc…
-
``````
What steps will reproduce the problem?
1.Try to convert a bam file that contains e.g. the following line:
HWI-EAS225:6:114:1253:343#0 16 10 3185842 255 56M6158N19M
* …
-
When I used bam file which generated by snapr for cufflinks, I got the following error:
BAM record error: found spliced alignment without XS attribute.
I did some research and found that was because o…
-
bam_vs_bed currently treats alignments as starting at the start location and continuing to the end location, irrespective of if the alignment is split (/spliced).
Adding split to the bedtools inters…
-
```
What steps will reproduce the problem?
1. Start with an rna-seq bam file
2. Query a region that includes spliced reads overlaping a position using
pysam.pileup()
3. Try to get the allele frequenc…
-
Hi,
I'm using the assembled transcripts GTF with StringTie to run cuffmerge,but i get error as follows:
[14:42:00] Loading reference annotation.
[14:42:03] Inspecting reads and determining fragment …
-
I have mapped alignments with STAR (stranded data, dUTP, PE101), that lack the XS flag. I guess that is reason why assembly step fails:
```
java -Xmx6g -jar ~/bin/IsoSCM-2.0.9.jar assemble -bam WT.ba…