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Answer: Annotating file using bcftools
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p
Convert fastq.gz to fastq.bgz
Comment: ggrepel function: geom_text_repel()
Comment: Missing protein (VEGF-A) in String db
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Recent Replies
Comment: What's next after GATK variant calling pipeline?
by
Michael
54k
The link didn't work for me. After getting variants from HaplotypeCaller, there are a lot of different options for follow-up analyses, but …
Comment: Getting differential ChIP-seq peaks between conditions after calling consensus p
by
ATpoint
82k
That having said, linked paper and its authors developed the csaw package over at Bioconductor that uses a window approach to avoid peak ca…
Comment: Getting differential ChIP-seq peaks between conditions after calling consensus p
by
Ian
6.0k
Really interesting answer. I had missed that paper and will digest it asap. I usually use DiffBind, but recently have been looking into p…
Comment: Annotating file using bcftools
by
kl
▴ 10
It worked with this bcftools index -t $DATADIR/cpro_imputed_hrcgrch37.R2_0.3.vcf.gz bcftools annotate \ -a $RefGenomes/All_20180423.vcf.gz…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
This is true. However, there are a number of studies that have done bioinformatics analysis in whole blood to see if there is a possibility…
Comment: ggrepel function: geom_text_repel()
by
sooni
▴ 20
Thank you for help! I solved the probelm with the package.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
I have checked the quality of the arrays using PCA and Boxplot (images attached) and some of the samples may deviate a little but perhaps n…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
the nt database was extracted, and this is latest version of nt database in ncbi and blastn with version 2.15. I used many query file.fast…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
they don't have clear answer for this problem. I run all subset of this data to find out error subsets database but it seem not any error i…
Comment: ggrepel function: geom_text_repel()
by
zx8754
11k
There is a dedicated package for this, see - https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html
Comment: Sam file Header problem
by
Pierre Lindenbaum
161k
-R "@RG\tID:sample\tSM:sample\tPL:Illumina" where is this '@RG' in the header anyway ? are you sure you're handling the correct fil…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
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Pierre Lindenbaum
161k
it looks like the same error.
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thankyou so much Andres for your reply. I think I got your point, just have a couple of quick questions to make it more clear . 1) I do n…
Comment: Duplicated reads (IDs) from nanopore sequencing
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njornet
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I've looked into it and one of the reads with a supplementary alignment has the representative alignment aligning to the + strand and being…
Answer: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
by
kuttibiotech2009
▴ 30
Hello friends, Thank you for your feedback. I understand that the post may not directly relate to bioinformatics. My aim was to share …
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