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This is not really a bug as the documentation clearly states how deduplicate_bismark expects UMIs to be handled, but it is an easy mistake to make.
As documented in deduplicate_bismark, Bismark expe…
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Hi,Alex
Thanks for reading my question:
here are my parameters:
STAR --runThreadN 8 \
--genomeDir /home/dii/data/ref_gene/mouse/STAR_anno \
--readFilesIn /home/dii/data/GEGA/raw_RNAseq…
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### Ask away!
The PCR-cDNA barcoding kit, incorporates UMIs with the strand switching primer into the strands which are then sequenced. Is there a point in this pipeline that takes these UMIs into ac…
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I have a whole genome em-seq methylation library with dual indexes as well as methylated UMI's at the beginning of each R1 and R2. These are from Twist and were used to make EM-seq libraries. I am not…
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Hi There,
Thanks for samblaster, it's such a great tool. I wonder if you have considered supporting unique molecular identifiers at all? bcl2fastq supports adding them to the read name. So if a standa…
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### Description of feature
I have WGS data generated with a library prep that includes UMIs ([Claret Biosciences SRSLY for FFPE](https://www.claretbio.com/products/kits).
The current pipeline code d…
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I hope this message finds you well. I am currently encountering some difficulties while running a program, and I would greatly appreciate your assistance in resolving these issues.
> library(SingCe…
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Dear Velocyto Team,
It looks like that version `0.17.10` introduced a bug into `run_smartseq2`.
When running
`velocyto run_smartseq2 -o OUTPUT -m mm10_rmsk.gtf -e 35_rmsk ../bam-star/35/Aligned…
d-j-k updated
6 years ago
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I was wondering if you had considered merging UMIs that might be erroneous copies, eg as outlined in this [blog](https://cgatoxford.wordpress.com/2015/08/14/unique-molecular-identifiers-the-problem-th…
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With Python 3.7:
```
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/rthuang/anaconda3/envs/XCL-PRE/lib/python3.7/multiprocessing/pool.py", line 121,…