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Hi,
Just wondering what is the strandness of the transcript sequence in flair.collapse.isoforms.fa? Is all the sequence presented as + strand from the reference genome? Or the sequence is already p…
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We look at a lot of Nanopore direct RNA-seq and have found it nice to look at reads stacked in descending order of length. For positively stranded reads, this is easily accomplished by sorting by star…
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Hello,
I have run ShapeMapper2 to calculate map data for two 1500-nt overlapping amplicons. During library preparation they were fragmented, so not all obtained reads contain the sequence of amplic…
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Here are my commands. I am running it two different ways. First, using the reference genome:
`minimap2 --MD -t 50 -ax splice -k14 -uf /home/banskotan2/Reference/grch38/Homo_sapiens_HG38_GRCH38_10…
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Hi DENA team! I' d want to know how you get the 4685 miCLIP sites identified in Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification, while I found th…
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File `semmedVER43_2022_R_PREDICATION.csv` contains 117,589,597 rows. After removing rows with `SUBJECT_NOVELTY == 0` or `OBJECT_NOVELTY == 0`, 81,282,024 rows remained. Among those rows, there are 303…
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Dear Dr. Dooley,
Good day. I am trying to run your scripts to find TracrRNA from my bacterial genomes. I have just started running the scripts, but I found an error that says: FileNotFoundError: […
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
```python
>>> import sys; print(sys.version)
3.9.7 (default, Sep 16 2021, 13:09:58)…
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#160
I am having a similar problem. I am running the FLAIR collapse on 41 samples (direct RNA seq) but after two day run the analysis give me FAILED to write result error after the minimap2 alignmen…
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I tried to run JAFFA on some of our larger fastqs (8 Gb Read1 + 8 Gb Read2 ), which timed out after 12 hours. I can raise the time limit with no problem, but i also noticed that the average and maximu…