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Tag: AfterQC
scanpy problem for empty cells
Hello everyone, I encountered a problem when I use scanpy analysis my data. When I tried to remove scrublet, and then I encountered following error: filtered out 42144305 cells that have less than 200 genes expressed Running Scrublet normalizing counts per cell /rsrch4/home/canbio/conda/envs/scvi-env/lib/python3.11/site-packages/scanpy/preprocessing/_normalization.py:197: UserWarning: Some cells have zero counts warn(UserWarning(‘Some…
AfterQC 0.9.7-foss-2020b-Python-2.7.18 (for BlueBEAR, BEARCloud VMs, and CaStLeS VMs)
AfterQC 0.9.7-foss-2020b-Python-2.7.18 Automatic Filerting, Trimming, Error Removing and Quality Control for fastq data. Accessing AfterQC 0.9.7-foss-2020b-Python-2.7.18 To load the module for AfterQC 0.9.7-foss-2020b-Python-2.7.18 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs): module load AfterQC/0.9.7-foss-2020b-Python-2.7.18 BEAR Apps Version 2020a More Information For more information visit…
Difference in fastqc output after trimming with fastp vs afterqc
Forum:Difference in fastqc output after trimming with fastp vs afterqc 0 Hello, Upon trimming ddrad fastq files with fastp, the per base sequence content is still a ‘red cross’ but after using afterqc, the same is now yellow with an exclamatory mark, indicating it has improved. But upon using stacks,…
Novel mutation of extracellular matrix protein 1 gene in LP
Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China Correspondence: Jianyou Wang, Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, People’s Republic of China, Email [email protected] Abstract: Lipoid proteinosis (LP) is a rare autosomal recessive…
Is it normal for RCorrector to remove millions of reads?
Is it normal for RCorrector to remove millions of reads? 0 I’m trying to build De Novo transcriptomes for unsequenced plants to do sequence analysis. I’m trying to choose a tool for my first pass of quality filtering after running FastQC on my raw reads. I’ve tried AfterQC and RCorrector….