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Answer: How to import conda environments to Rstudio?
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
A: Extracting reads with low mapping score from Bam file
A: Samtools mpileup of soft-clipped alignment behaves non-deterministically?
Answer: convert .bed format to .txt format
Answer: convert .bed format to .txt format
Answer: Extract nucleotide sequence from a RefSeq Transcript ID
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Comment: CPTAC data download, transcriptomics
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GenoMax
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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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Shred
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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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Rob
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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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Antonio R. Franco
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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?
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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
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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
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gogo21
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yeah I am also getting the same issue is this issue due to wrong path provided ?
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BioRyder
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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
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Bianca
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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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