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I'm trying to align a slew paired end 100 bp transcript sequences to a reference genome from NCBI with a gff (converted to gtf) file. However, my % of reads unmapped: too short is coming up in the 60%…
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Input data file a: Aligned reads file obtained from mapping short reads to a reference genome
Short reads means that only gDNA reads, Right?
Thank you very much.
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**Question or Expected behavior**
I have a reference genome obtained after CANU assembly, purge_dups and long reads polishing with arrow. I'd like to polish with short reads using Next_polish.
Shoul…
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When reads lengths are shorter than adapter lengths, the detect command does not do as good a job of identifying the full-length adapter sequence as FASTQC.
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Hi,
I am getting high percentage of unmapped reads for my paired end RNA reads.
Fastqc looks fine with no adaptors to trim and when I mapped my paired end separately, they percentage are the same…
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I am aligning human stranded RNA-seq data (PE 101) from ~30 samples to the `chm13v2.0` assembly with the command below
and am experiencing 15-28% of unmapped, "too-short" reads.
```
STAR --runThrea…
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When `DAQmxReadAnalogF64` with `DAQmx_Val_GroupByChannel` returns fewer samples than requested, it squashes the valid samples together at the beginning of the buffer. The way that `nidaqmx.Task.read` …
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Somehow I'm ending up with a very low number of duplex reads after using Dorado duplex basecalling with the following command (used the ligation sequencing kit V14 SQK-LSK114):
`dorado duplex dna_r…
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When I use STAR for alignment, many reads do not align. How can I resolve this? THANK YOU !
below is my parameter:
STAR --runThreadN 15 --runMode alignReads --quantMode TranscriptomeSAM GeneCoun…
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Hi vg team!
I'm trying to use **vg giraffe for mapping very short paired-end reads (36bp) against a pangenome**.
I tried running this command line
```
> vg giraffe -M 10 -x ${panIdxPath}/$…