-
Hello,
When trying to align reads to to the end of a gene, kallisto is unable to pseudoalign this read. However when using the --single-overhang option, pseudoalignment occurs.
My question is …
-
I am trying to realign SC3 sequencing data from a published paper (method: https://pubmed.ncbi.nlm.nih.gov/25722368/), and it seems to do so they require the GTF/GFF3 file used for reference annotatio…
-
command:
```
kallisto pseudo -i ~/data/cDNA/Homo_sapiens.GRCh38.rel79.cdna.all.idx -o /home/others/xli/scRNA/p20/output2/ --umi -b /home/others/xli/scRNA/p20/output/umi_read_list.txt --pseudobam
``…
-
Hi,
I want to use ABIS for deconvolution of the RNA-Seq profiles generated from the whole blood ( only RBCs are removed by RBC lysis buffer) remaining all cells are their. I have run premilinary ana…
-
Hi,
For SC5P chemistry, I should be able to define 0,0,16:0,16,26:0,26,0 for the 1st read and 1,0,1:1,0,1:1,0,0 for the 2nd read in -x parameter.
Can this be done?
Best
Pasi
-
WIth typical kallisto pseudoalignment rates of ~70% for human total ribo-depleted RNA libraries, an obvious question is what the remaining 30% of reads represent, especially when aligners like hisat2 …
-
Hi there,
I'm currently evaluating whether we could use kallisto/pizzly for fusion gene prediction. However, for some samples I realized that kallisto is somehow freezing at BAM indexing (waited for …
-
I have put a small example on [this gist].(https://gist.github.com/winni2k/64efa2e354a70a72d8a70a5ac373cc49)
When I run `run.sh`, I get the following output:
```bash
0 reads pseudoalign
[build…
-
Hi I am pretty new to kallisto/bustools so thank you for your help in advance. I followed directions from this issue/Google collab: [Issue #75](https://github.com/BUStools/bustools/issues/75)
I ra…
-
I downloaded the latest binary for my linux server and created a simple reference with 1 sequence in it.
```
> kallisto version
kallisto, version 0.44.0
> kallisto index --index myref myrefere…