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Some of the sequences are missing from the result file that are present in the source file.
#### Source File
```
>FJ475559.1 Uncultured Suillaceae clone AhedenA42 18S ribosomal RNA gene, partia…
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Hi, developer,
Thanks for creating such efficient software. I have used it to find the 16S rRNA hits in my de-novo assembled genome bins. My purpose is to search for archaea and bacteria, so I run th…
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seems like there is a missing copy of rRNA in assembly in KN99. filter out this depth variant call.
(provide a region filter list option)
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I think hisat is not handling ribosomal RNA reads very well (see image). Neither are Star or Tophat2.
Tophat also finds a bunch of strange splice junctions (top)
Hisat is finding a bunch of splice jun…
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Hi,
I am using this pipeline to reanalyze some data from Illumina Novaseq PE250bp.
And I have noticed that in this paper , they sequenced at Hiseq PE250bp (McNichol, J., Berube, P., Biller, S.…
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Hi,
What parameters do you suggest changing when working on Illumina short-amplicon reads of COI genes?
For example, would you:
- `SelfConsist = TRUE` instead of proving 16 × 41 Transition prob…
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Hi,
First of all, thanks for developing this tool!
I have a few metagenomic samples from which I've estimated the number of couple of reads mapping in proper pair to the SSU rRNA genes present in …
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There are quite a few transcripts annotated as 'ncRNA'. However according to the ID mapping, it seems they could be annotated further as tRNA, rRNA etc.
```
$ zcat homo_sapiens.GRCh38.gff3.gz | g…
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Since most folks use GTFs for RNASeq, but `CollectRnaSeqMetrics` uses a refflat file, it would be nice to have a tool that can convert GTF to refflat, and then we can update `CollectRnaSeqMetrics` to …
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Hello, Prof. Zhou,
I'm new to bioinformatics, I want to do RNA-seq analysis with PBMC COVID-19 data of your research. But I can't find the rRNA sequence for remove rRNA. Could you tell me where can …