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blacktomato27
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Recent Replies
Comment: is it .impute2 format equal to .gen format
by
Kevin Blighe
73k
Hi, yes, I feel your frustration. This qctool, I have found, just does not work. I checked my code from 2019 and I had commented out the pa…
Answer: Statistics analysis of assembled genome from PacBio HiFi reads using Hifiasm
by
wrowell
•
0
You can get N50/NG50 from https://github.com/lh3/calN50.
Comment: is it .impute2 format equal to .gen format
by
SHN
▴
20
Thank you for your response. I have gone through all the links you provided all and above and I did not find any solution to my issue.
I …
Answer: Comparison of module expression across WGCNA networks
by
Kevin Blighe
73k
I posted this as an answer outside of Biostars:
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There is no correct or incorrect answer to this. To me, i…
Answer: WGCNA cannot be done to compare two conditions?
by
Kevin Blighe
73k
I posted this as an answer outside of Biostars:
--------------------
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There is no correct or incorrect answer to this. To me, it mak…
Comment: Statistics analysis of assembled genome from PacBio HiFi reads using Hifiasm
by
Dave Carlson
▴
620
Quast and BUSCO would be my initial suggestions, but it really depends on what specific stats you're looking to compute.
Comment: what is the deal with bioconda?
by
xiaoleiusc
▴
70
thanks. it works great and solved the problem!
Comment: STAR alignment issue
by
srinivasa rao
•
0
Hg19.gtf looks good, this is the same file I used for my index , 828,000kb , this file doesn't need to be in Index directory correct ?
Comment: over 900 million bases in CCDS regions?
by
Yiming
•
0
The second screen of USCS Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=1109848749_gHXtAmBqKaR1UOA191fS812ba8pn&clade=mamma…
Comment: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Ge
by
Cyriac Kandoth
5.5k
Correct. The BED files in https://www.synapse.org/#!Synapse:syn1695394 are all samples that underwent DNA-sequencing and variant calling.
Comment: over 900 million bases in CCDS regions?
by
Yiming
•
0
To my understanding, the data here, especially the newer ones, are built on GRCm38, while my data uasd hg19 as reference genome
Comment: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Ge
by
rebeliscu
•
0
To clarify: if a sample is listed as a bed file, it can be assumed that it was then used for variant calling?
Answer: Aligning PacBio hifiasm CCS to reference genome using pbmm2
by
gconcepcion
▴
60
This is just a legacy warning (pre-HiFi data) and will not prevent the command from completing.
In general, assemblies generated from H…
Answer: is it .impute2 format equal to .gen format
by
Kevin Blighe
73k
This thread is accumulating traffic, so, I thought to provide some guidance.
From what I can gather, *qctool* became 'outdated' over time.…
Comment: over 900 million bases in CCDS regions?
by
Ram
33k
What did you pick in the second screen - One entry per gene or per coding exon or something else?
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