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I've had a bug report against our software which appears to be an underlying bug in the htsjdk parser for BAM files. The read which fails to parse is a spliced read with a huge intron in it (226Mbp).…
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I am using stringtie 1.0.2 on a ubuntu server, which has 32GB memory and 32GB swap, 8 core cpu. When I am processing a bam file generated by HISAT, the stringtie process always be killed by linux kern…
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I was wondering why
nuclear mRNA splicing, via spliceosome
could not be called "mRNA splicing, via spliceosome"
From what I can see, unless I am missing something, this type of spliceosomal splicin…
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I've been dealing with long runtimes on some code, and finally tracked the source down to bedtools behaving oddly.
I have a sorted BAM file of RNA-Seq reads (HG00097_mapsplice_alignment.sort.bam), an…
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Hi
This is a little bit complex to reproduce. But here goes.
If you have a long sequence of lets say 30 items. Scroll down to the very bottom.
Now execute an event that will clear the sequence and…
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When running RNAseq analysis using STAR and strandedness, the XS attribute is not set by STAR (missing from --outSAMattributes NH HI NM MD AS). This leads to cufflink errors: BAM record error: found s…
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``` text
chr1 161192312 C A 2,0,110,118 0.991304347826
```
という結果をIGVで可視化すると、
![2013-12-31 13 45 09](https://f.cloud.github.com/assets/1855860/1825810/d3e93eae-71d6-11e3-8d35-…
soh-i updated
10 years ago
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Hi,
I've upload a RNA-Seq bam file in a local instance of jbrowse 1.8.1.
The spliced reads are not well positionned on the reference. It seems that the alignments having a soft clip at the begining o…
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RefSeq [annotation](http://www.ncbi.nlm.nih.gov/nuccore/NM_001127) of transcript NM_001127 of gene AP1B1 presents a "small" exon (9nt) at position (1-based inclusive, relative to the transcript sequen…
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In the gene CEACAM7, a 8nt-long prefix of RefSeq NM_006890 is not correctly aligned due to a single base mismatch in the previous position (`T``G`). Since the length of factor before the mismatch is s…