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Recent Replies
Comment: SRA not splitting when trying to download fastq
by
tomas4482
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270
I've demonstrated `fastq-dump` is the only option. Should you try the suggested script first? I don't know what command your coworker used …
Answer: 10X genomics single cell
by
MohammadAlkadi
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70
Usually, biological pathways are analyzed for clusters, not individual cells since clusters are supposed to have similar cells and therefor…
Answer: perl can't see path problem
by
Carambakaracho
★
3.0k
Perl can't see [the moose module][1]:
```
conda install -c bioconda perl-moose
```
[1]: https://anaconda.org/bioconda/perl-moose
Comment: Batch effect correction & normalization after training/test split for gene expre
by
BioInfoBeginner
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40
Are you hoping to account for known batch effects (i.e. you have metadata which tells you some of the experiment was done on one day and th…
Comment: Large intron or bad read polishing of tandemly duplicated genes?
by
Ben Nestor
•
0
Thanks for the answer!
Here's a diagram I made previously which explains it. Only the first half of the gene is shown, but there is anothe…
Comment: SRA not splitting when trying to download fastq
by
Emily
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20
I did the prefetch command to download sra filed and then did ~/sra_data/SRR19687957$ fasterq-dump SRR19687957 --split-files
I also had my …
Comment: SRA not splitting when trying to download fastq
by
Emily
▴
20
~/sra_data/SRR19687957$ fasterq-dump SRR19687957 --split-files is the command that I ran but still comes out single end read file
Could yo…
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
▴
740
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
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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…
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