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bioinfo_ga
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Pierre Lindenbaum
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Recent Replies
Comment: Getting same value for start and end position, "DNA methylation"
by
ATpoint
72k
That's a comment, not an answer, please use `ADD COMMENT`.
Comment: Getting same value for start and end position, "DNA methylation"
by
bioinfo_ga
▴
50
Are you working on bisulphite kind of data or chipseq ????
Answer: How to calculate TPM from featureCounts output
by
bioinfo_ga
▴
50
hi ,
You can use a python package rnanorm [https://pypi.org/project/rnanorm/]. The input required are your read count values from feature …
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by
by
biofalconch
▴
580
Hey, if you arelady have the barcodes, you could use samtools
`samtools view -h -b -f CB:Z:TAAGAGATCCTATGTT > TAAGAGATCCTATGTT.bam`
Hope…
Answer: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by
by
biofalconch
▴
580
Here is a code that should work, but just like everyone else in the comments I'm a little confused why would you need to separate them:
…
Comment: CNNScoreVariants Error
by
Pierre Lindenbaum
154k
check you have a complete environment for GATK , including the python module "keras". https://gatk.broadinstitute.org/hc/en-us/articles/360…
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by
by
Cathal
•
0
Did you have any luck in splitting the BAM file based on the 10x cell barcode? I would like to split a BAM file based to only include 5 spe…
Answer: Getting same value for start and end position, "DNA methylation"
by
ATpoint
72k
genomation is based on GenomicRanges which uses 1-based coordinates. https://www.biostars.org/p/84686/
Since a single CpG has a length o…
Comment: Gene enrichment analysis
by
ATpoint
72k
I cannot speak for this package but I recommend clusterProfiler where the universe argument isindeed all tested genes so your background.
Answer: Finding Enhancers using Genomation library
by
ATpoint
72k
You cannot derive enhancers from methylation profiles. Enhancers are regulatory elements, and they either are methylated or not. There is l…
Answer: convert data frame with character column to data frame with integer column
by
Basti
★
1.5k
Cross-posted and answered there : https://stackoverflow.com/questions/76388032/convert-data-frame-with-character-column-to-data-frame-with-…
Comment: Getting same value for start and end position, "DNA methylation"
by
Basti
★
1.5k
Your question lacks precision, we do not know what you are talking about
Comment: Gene enrichment analysis
by
Meisam
▴
180
If you want to find enrichment of your selected genes versus the superset of all genes detected, then yes you mean the background. And to d…
Comment: WGCNA Trait File Issues
by
LChart
2.6k
The NAs are coming from the fact that each 'Sample' (which I assume is a unique identifier for a sample) is not actually a number and so th…
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