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Comment: Retrieve a % coverage for each transcript
Inconsistency in SNP detection pipelines for multi-sample analysis
Answer: bwa 0.7.18 download to fix compile fail with GCC 10
Comment: Can I readmap short reads to rDNA references?
Answer: Merging vcf files with bcftools ([E::get_intv] Failed to parse TBX_VCF, was wron
C: Find Transcription factor binding site for a gene list
Answer: ESTIMATE tumor purity
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Recent Replies
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
LChart
3.9k
I don't think this approach will give you what you want. Combining multiple tissues in the way you are suggesting will result in a positive…
Comment: Supergnova stuck in tutorial
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Murat
• 0
Hi Gerard, I am also using the tutorial and found your answer. The ftp links are not working any longer; is there any other source to downl…
Comment: Method to detect genome doubling
by
Zhenyu Zhang
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This is only true for pure WGD that is not distinguishable using NGS. However, in most tumor evolution, a WGD event is often followed b…
Comment: Questions about a bug when transferring cram file to bam file
by
Pierre Lindenbaum
161k
> Interesting, does this mean I cannot find the reference of this cram file? it means that the REF you're using is not the one that was …
Comment: How to get the reference panel for UKBB
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bk11
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Please check this link [here][1]: ![https://www.ukbiobank.ac.uk/enable-your-research/about-our-data/genetic-data][2] [1]: https://www.…
Comment: Retrieve a % coverage for each transcript
by
GenoMax
141k
Past threads that should be useful: https://www.biostars.org/p/287692/<br> https://www.biostars.org/p/9556576/
Comment: Can I readmap short reads to rDNA references?
by
aniigodwinn
• 0
Thank you! I will try this now.
Comment: How can I solve this error?
by
GenoMax
141k
https://www.biostars.org/u/144260/ : It is useful to add some description of what you are trying to do? Which software you are using (metal…
Answer: Pruning Phylogenetic Trees and Bootstrap Values
by
Klaus S
▴ 150
Dear Zeng, you have to also prune the bootstrap trees and and reassign the bootstrap values to your small tree given the now smaller bo…
Comment: Can I readmap short reads to rDNA references?
by
GenoMax
141k
> I have some reads that I want to assemble but there is no genome available for this species You don't need a genome for assembling read…
Comment: Questions about a bug when transferring cram file to bam file
by
me
• 0
Thanks. I only need the fasta file because I am working on individual sequencing data. Do you have any idea about directly transferring cra…
Comment: Questions about a bug when transferring cram file to bam file
by
me
• 0
Hi, I have checked that the cram file prints ok. And yes, it is a dot... Interesting, does this mean I cannot find the reference of this cr…
Comment: Which experiments generate Position Frequency Matrix?
by
arriyaz.nstu
▴ 30
That was very helpful. Thank you for your reply.
Answer: Sheep reference genome remapping coordinates
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colindaven
6.3k
If you want to remap genes and have a gff3 file, then Liftoff would be a decent recommendation https://github.com/agshumate/Liftoff It is…
Comment: Editing Human Reference Genome by adding a CDS
by
Michael
54k
If it's a plasmid in a transfected cell, I would indeed add the whole plasmid sequence including the insert. Most likely you have gotten a …
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