User: dz2353

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dz235370
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Posts by dz2353

<prev • 25 results • page 1 of 3 • next >
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How to identify lncRNAs from a probe set?
... Hi, there, I downloaded a microarray from the GEO database. The platform is GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]. I used a package from Bioconductor to transform the prob id to Ensembl id. After that, I downloaded the lncRNA annotation from GENCODE, ...
rna-seq written 6 weeks ago by dz235370
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Comment: C: Question about how to transform RSEM expected_count of TCGA TARGET GTEX to integ
... Yep, I did (2^x)-1 but the result is not an integer format cause the scale. I will round them. Thanks a lot! ...
written 6 weeks ago by dz235370
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Question about how to transform RSEM expected_count of TCGA TARGET GTEX to integers?
... Hi, there I downloaded RSEM expected_count data of TCGA TARGET GTEX from UCSC Xena to perform differential expressed analysis. I noticed the unit is log2(x+1), but I failed to turn the data into integers. The input of DESeq2 should be a matrix with integers. Any suggestions? Thanks in advance! Bes ...
rna-seq written 6 weeks ago by dz235370 • updated 6 weeks ago by i.sudbery5.0k
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How to deal with the .sra.vdbcache files after downloading a sra file?
... Hi, there I have downloaded some .sra files by using prefetch command from GEO database. After that, I found some cache files in the same folder. The extension is .sra.vdbcache or .sra.vdbcache.cache. So I was wondering if I could delete them or how to deal with them? Does it mean that I do not dow ...
rna-seq written 10 weeks ago by dz235370
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Comment: C: How to assign the result of a command to a variable in shell script?
... Thank u for your reply in detail and I make sense how does it work! ...
written 10 weeks ago by dz235370
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Comment: C: How to assign the result of a command to a variable in shell script?
... I tried but the output was {i}.fastq. The command basename provided by genomax works well. Thanks for your answer! ...
written 11 weeks ago by dz235370
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Comment: C: How to assign the result of a command to a variable in shell script?
... The command basename works well, thanks so much! ...
written 11 weeks ago by dz235370
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Comment: C: How to assign the result of a command to a variable in shell script?
... Nope, I think the input is SRR222423.fastq and I split it by using dot. After that, I use -f1 to choose the first part then I get SRR222423. Is it correct? ...
written 11 weeks ago by dz235370
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Comment: C: How to assign the result of a command to a variable in shell script?
... Actually, I just want to test if this shell script works. There is only one .fastq file in the ./single directory named SRR222423.fastq. The input of trimming is SRR222423.fastq. And I want to get the output in the same directory with the name like SRR222423_clean.fastq. No error appears. The output ...
written 11 weeks ago by dz235370
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How to assign the result of a command to a variable in shell script?
... Hi, there I want to assign the sample id to the output of trimmomatic but I failed. The name of the output is _clean.fastq and the variable j is missing. How can I figure out this issue? Thanks in advance! for i in ./single/*.fastq do echo ${i} j=$(echo ${i} | cut -d "." -f1) j ...
rna-seq written 11 weeks ago by dz235370

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