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Recent Replies
Comment: how can i filter a sam file from a paf file
by
colindaven
4.6k
Just save yourself a lot of pain and learn to filter the sam/bam file efficiently. It is much more of a widespread standard than PAF.
Comment: Snakemake workflow for trimmomatic
by
GenoMax
127k
Please accept this answer (green check mark) to provide closure to this thread.
Comment: syntax errors when running part3 all-against-all
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Sofia
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When I started with the gz all-vs-all files for CHICK and ANOCA and started oma, everything ran fine, I got output. Then, in the same direc…
Comment: Quality control of Chip-seq data (NRF and PCB)
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michelafrancesconi9
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Can you explain me better? Because for the NRF I do :
a) samtools view -c .bam
b)samtools view -c -F 260 .bam
then b/a
and as a bam fi…
Comment: pyCirclize - Circular visualization in Python
by
karenkvn
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40
Thank you for responding so quickly - this works perfectly!
Comment: pyCirclize - Circular visualization in Python
by
moshi
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Please install Biopython with v1.80 or higher.
If biopython>=1.80, there should be no errors.
Comment: Gene family classification using RNA-seq data
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Dion
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well, I have been given the task to retrieve gene family/categorization. I found sveral papers on family classification, but no actual pack…
Comment: pyCirclize - Circular visualization in Python
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karenkvn
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Thank you for this wonderful programme! I am plotting a bacterial chromosome and find that when I plot the NC_000913 chromosome using the e…
Comment: SKAT in R
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Eliza
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@acvill can you sujjest maybe pther tools , methods for this ? ( also for every SNP i have data how many patients had the hetro/homozygous…
Comment: TCGA-BRCA tissue and RNAseq problem
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pinheirofabiano
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Go to https://portal.gdc.cancer.gov > Exploration > select TCGA and the cancer type you want > select case ID to download the files and hav…
Comment: Snakemake workflow for trimmomatic
by
antoine.fauchois92
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Thank you very much for your reply ! It's working now !
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Eliza
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@lchart I'm sorry for asking another of questions but I'm new to this field , can you please explain a little more how to use SKAT , saige…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
dare_devil
★
1.7k
similar question [here][1], [here][2] and [here][3]
[1]: https://support.bioconductor.org/p/54838/
[2]: https://support.bioconductor.…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
dare_devil
★
1.7k
@genomax I have used the same platform file only. If you look at probe id and their corresponding `Gene Symbol` or `ENTREZ_GENE_ID` you can…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
GenoMax
127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned.
[1]: https://www.ncbi.nlm.nih.go…
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