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Answer: SRA not splitting when trying to download fastq
A: Publicly-available Metabolomics Data
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Reading in input file into a Snakemake pipeline
Answer: Reading in input file into a Snakemake pipeline
Bedtools intersect PE BAM reads
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Comment: SRA not splitting when trying to download fastq
by
tomas4482
▴ 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 …
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Usually, biological pathways are analyzed for clusters, not individual cells since clusters are supposed to have similar cells and therefor…
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Perl can't see [the moose module][1]: ``` conda install -c bioconda perl-moose ``` [1]: https://anaconda.org/bioconda/perl-moose
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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…
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Ben Nestor
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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
▴ 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
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~/sra_data/SRR19687957$ fasterq-dump SRR19687957 --split-files is the command that I ran but still comes out single end read file Could yo…
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[**As noted here**][1] the transcriptomic data is harmonized using GDC pipelines: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines…
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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…
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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…
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Hi it is not RSEM format and every file has different columns that you can see in the image above. such as tpm, fpkm
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If using RNA, I would expect not having the complete set of genes being expressed
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Yes, I was able to view it. Thank you.
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thank you!!!!!!!!!!! this was so helpful. makes me think we convenient browser based tools etc. i really appreciate you.
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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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