User: V

gravatar for V
V110
Reputation:
110
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Trusted
Location:
UK/London
Last seen:
7 months, 2 weeks ago
Joined:
4 years ago
Email:
k*******@kcl.ac.uk

Posts by V

<prev • 61 results • page 1 of 7 • next >
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Comment: C: Downloading single cell data from NCBI
... Realistically I dont mind either way, I want to do is realign the data to mm10 and generate a count file that has every cell in the experiment so I can pass it into Seurat etc. Would you happen to know of a way around this? My biggest issue is why are all the cells smushed into 1 file it looks like ...
written 7 months ago by V110
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Comment: C: Downloading single cell data from NCBI
... Hello, I seem to not have the fastq command in my samtools for some reason even though I'm at the latest version. I've ran samtools bam2fq on the bam file and it's only generated 1 fastq file, shouldn't I have two per cell? ...
written 7 months ago by V110
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Comment: C: Downloading single cell data from NCBI
... Thank you for your help, I will have a look at downloading the uBam file and see what the samtools fastq function does to it. ...
written 7 months ago by V110
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Downloading single cell data from NCBI
... Hello, I am trying to download a single cell RNAseq run from NCBI. It is SRR7898910 also found here [Link][1] [1]: https://www.ncbi.nlm.nih.gov/sra/SRX4736338[accn] I try to download the data using the NCBI recommended way of downloading the SRA file using prefetch and the using the following ...
ncbi fastq-dump rna seq single cell written 7 months ago by V110
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Comment: C: ChIp-seq RNA-seq overlap
... by that you mean like a GTF file you use for RNAseq analysis? ...
written 13 months ago by V110
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Comment: C: ChIp-seq RNA-seq overlap
... Sorry for the naive question, but when doing computeMatrix on the ChIPseq file, what do you use for -R. I keep getting this error: computeMatrix scale-regions: error: argument --regionsFileName/-R is required I'm guessing it wants the bed file with the peaks - but isn't the point of this appro ...
written 13 months ago by V110
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ChIPseq vs RNAseq results comparison
... Hello, I have a number of RNAseq bigwigs and ChIPseq bigwigs and would like to compare overall how counts in one location compare to counts in the same location in the contrasting experiment. To plot literally something like the figure here : https://www.nature.com/articles/nn.4532/figures/14 Doe ...
chip-seq rna-seq written 13 months ago by V110 • updated 13 months ago by Devon Ryan91k
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Comment: C: Bash Script Loop Help
... Sorry for the confusion, had mixed version of it. All sorted now with your post. Thanks alot! works like a charm. ...
written 17 months ago by V110
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Comment: C: Bash Script Loop Help
... I've tried that but it doesnt work sadly, the echo returns: hisat2 -x mm10idx -1 WTCHG_465974_296190_1_val_1.fq.gz -2 WTCHG_465974_296190_1_val_2.fq.gz -S WTCHG_465974_296190_1_val.bam The loop as is thinks that the R2 finishes in "_1_val_2.fq.gz" but it finishes in "_2_val_2.fq.gz" the issue ...
written 17 months ago by V110
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Bash Script Loop Help
... Hello, I'm trying to run hisat on loop and I've been trying to modify an existing loop I had set up but can't get it to work with my new file names. My R1 is called WTCH_1_val_1.fastq and my R2 is called WTCH_2_val_2.fastq, where every time WTCH is actually a different value to distinguish the d ...
rnaseq loop bash written 17 months ago by V110

Latest awards to V

Great Question 13 months ago, created a question with more than 5,000 views. For Ensembl id to Gene name
Popular Question 13 months ago, created a question with more than 1,000 views. For Run Samtools on multiple files
Popular Question 13 months ago, created a question with more than 1,000 views. For Ensembl id to Gene name
Popular Question 13 months ago, created a question with more than 1,000 views. For fastq.gz Error: Not in gzip format
Student 13 months ago, asked a question with at least 3 up-votes. For Run mutltiple Fastq files on Hisat2
Popular Question 17 months ago, created a question with more than 1,000 views. For Ensembl id to Gene name
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Ensembl id to Gene name
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Run mutltiple Fastq files on Hisat2
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Ensembl id to Gene name
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Ensembl id to Gene name

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