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Hiya,
We are using Stringtie version 1.2.3 to compute the relative expressions of a few transcripts-of-interest, these are all single-exon transcripts. We found that most of the computed FPKM values…
tylim updated
7 years ago
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Hi Dear Dr. Kim,
I have 2 sequence reads archive and I want to do some RNA-Seq analysis on them.
Archive 1 : SRR1177960 (FastQ Files : SRR1177960_1, SRR1177960_2)
Archive 2 : SRR1177961 (FastQ Files :…
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Hello Alex,
I have encountered a situation that appears to me to be an incorrect STAR alignment that I would expect to be a somewhat common case in typical sequencing data sets. In short, in my …
ghost updated
8 years ago
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Hi,
I'm new to RNA seq and have some questions about the RNA seq output files. Is there any documentation available describing what's in the different outputs. E.g. I wonder about the difference betw…
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I'm surprised this isn't in while undefined and null are translated — the irony is that an undefined value is more likely to be indicative of a fault in application logic (author expected a value when…
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```
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…
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Hi,
I used hisat2 to map a few sets of RNA-seq reads to my reference genome, then used stringtie with all defaults to assemble, then used stringtie --merge to combine assemblies from different sets. …
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```
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…
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Dear authors and community,
recently I encountered a strange behaviour of bedCoverage which leads to very confusing results and I hope you can address this issue.
bedCoverage provides a function for…
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```
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…