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Hi hisat-3n developers,
Thank you for building this wonderful aligner!
I am working on using hisat-3n to align all the single-cell DNA methylome and multiome data generated by the [snmC-seq2 (D…
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Hello,
Thank you for developing this tool. I am trying to quantify transcript abundance using direct RNA seq reads after mapping with minimap2 to a transcriptome that I got using FLAIR and SQANTI too…
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```
What steps will reproduce the problem?
1. bamToBed -i foo.bam -split
on the following foo.bam file
@HD VN:1.4 GO:none SO:coordinate
@SQ SN:chr9 LN:124076172
@RG ID:sample1 P…
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```
What steps will reproduce the problem?
1. bamToBed -i foo.bam -split
on the following foo.bam file
@HD VN:1.4 GO:none SO:coordinate
@SQ SN:chr9 LN:124076172
@RG ID:sample1 P…
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When we use STAR to map the results of targeted sequencing we merge the gencode annotation with specific amplicons we use for targeted amplification. (We design primers close to polyA site in the 3-pr…
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Hi
I have a pangenome graph with 5 genomes generated from minigraph-cactus.
I'm currently indexing with autoindex to use mpmap and rpvg.
When aligning RNA-seq reads should I align each set of…
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Here are my command and log contents running `loompy fromfq`. It's stopped and I have no idea how to deal with that. I appreciate your help in this matter.
```bash
loompy fromfq sample.loom sample…
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Hi,
I recently ran into a very rare bug where I added U1,U2,U3,U4,U5,U6 and other snoRNAs to the genome and then defaulted the parameters to build the index. Then map my data on it. Then the program …
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This is a very cool project! There is a use-case for which we often have a need, and I wonder if it's enabled by `impg`.
Say I have an a collection of (RNA-seq) reads aligned against the genome (…
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Is my alignment file wrong? QoRTs.jar was executed in windows platform.
E:\junse>java -jar QoRTs.jar QC SAMP1.bam Bom7.gtf /output/
Starting QoRTs v1.2.42 (Compiled Fri Jun 2 12:23:55 EDT 2017…