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Recent Replies
Answer: Stringtie skips some reference genes
by
Antonio R. Franco
★
4.9k
If using RNA, I would expect not having the complete set of genes being expressed
Comment: convert .bed format to .txt format
by
rheab1230
▴
60
Yes, I was able to view it.
Thank you.
Comment: Extract nucleotide sequence from a RefSeq Transcript ID
by
Vincent Laufer
★
2.2k
thank you!!!!!!!!!!! this was so helpful. makes me think we convenient browser based tools etc. i really appreciate you.
Answer: Extract nucleotide sequence from a RefSeq Transcript ID
by
GenoMax
118k
Using [**Entrezdirect**][1]. Example for getting nucleotides 1101 to 1120.
$ efetch -db nuccore -id NM_001346941.2 -seq_start 1101 -se…
Comment: Using whole exome data from different protocols
by
m.bamajboor
•
0
I have similer question regarding the kits used for sequencing. I'm in a process of calculating the allele frequency of a group of samples,…
Comment: vcf2maf allele frequency not converting
by
hamrejr
•
0
Thanks. I am trying to get this on the maf from the vcf. So the command I am using is:
vcf2maf.pl --input-vcf .vcf --output-maf .vcf.m…
Comment: [RNAseq, featureCounts] Can paired-end data be processed as single end?
by
Luka
•
0
The IDs were indeed a problem, the processing worked after changing them. Thanks for all the help!
Answer: vcf2maf allele frequency not converting
by
Pierre Lindenbaum
147k
not tested but that could be:
paste <(bcftools view in.vcf | grep -v "^#") <(bcftools query -f '%INFO/AF\n' in.vcf)
Comment: Cannot install ATHLATES, issues with bamtools
by
gogo21
•
0
yeah I am also getting the same issue is this issue due to wrong path provided ?
Comment: Dual index barcode demultiplex issue
by
BioRyder
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220
Hello @devon / John Marshall
We have noticed some exceptional cases in our recent Novaseq run. We were using 'Dual Index Bio Scientific-…
Comment: R - cleanest way to calculate mean of a columnX in dataset1, columnZ in dataset2
by
Bianca
•
0
I found out why.
I was loading plyr after dplyr, that was my problem.
I removed library(plyr) from my code and only loaded (dplyr).
Now it …
Answer: merging data; remove extra rows
by
swbarnes2
12k
Is this RSEM format? Or some other format that txinport can handle?
Comment: R - cleanest way to calculate mean of a columnX in dataset1, columnZ in dataset2
by
Bianca
•
0
Hello,
that did not work.
It returned the mean value of all the data frames combined and the sum of all the data frames combined.
It return…
Comment: What is the best way to rank genes for GSEA?
by
hermidalc
▴
20
Just because you see something in published papers doesn't mean it's good or recommended, a lot of authors miss things or do not have a dee…
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