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Recent Replies
Comment: CPTAC data download, transcriptomics
by
GenoMax
118k
[**As noted here**][1] the transcriptomic data is harmonized using GDC pipelines: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines…
Comment: Determining strandedness of RNAseq samples from count data and understanding cou
by
ATpoint
64k
If you want to do that efficiently and systematically the I would take these CRAMs, convert some reads (maybe 1million or so) back to fastq…
Answer: Reading in input file into a Snakemake pipeline
by
Shred
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730
By doing
expand("0_reads_raw/{sample}_{read_set}.fq.gz", sample=SAMPLES, read_set=READ_SETS)
You're passing at the same time every p…
Comment: merging data; remove extra rows
by
Rob
▴
130
Hi
it is not RSEM format and every file has different columns that you can see in the image above.
such as tpm, fpkm
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
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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
▴
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 …
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