User: junsionglow

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junsionglow20
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1 month, 2 weeks ago
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2 months, 2 weeks ago
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j**********@gmail.com

Posts by junsionglow

<prev • 22 results • page 1 of 3 • next >
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Comment: C: DESeq2 - HTSeq-count txt error
... Must have been a silly question this one. Thanks h.mon! ...
written 8 weeks ago by junsionglow20
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DESeq2 - HTSeq-count txt error
... Hi, I am trying to perform differential analysis on my HT-seq-counts .txt files, using a command below's command, sampleFiles <- grep("CD39",list.files(directory),value=TRUE) sampleCondition <- sub("(.*annotated...).*","",sampleFiles) sampleTable <- data.frame(sampleName = ...
rna-seq written 9 weeks ago by junsionglow20 • updated 9 weeks ago by h.mon20k
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Comment: C: HT-seq - what is ideal?
... Thanks Devon! That makes sense. ...
written 9 weeks ago by junsionglow20
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HT-seq - what is ideal?
... Hi guys, I ran a HT-seq command and I would like to cross check with you guys. wonder what output is ideal? Below is the command htseq-count -f bam --idattr=gene -r pos /home/user/scratch60/STARresults/SRR7059136Aligned.sortedByCoord.out.bam /home/user/scratch60/NCBI_files/GCF_000001405.26_GR ...
rna-seq written 9 weeks ago by junsionglow20 • updated 9 weeks ago by Devon Ryan85k
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Comment: C: Very low unique mapped reads - STAR alignment
... Hi h.mon, it worked wonderfully, now I have over 80% unique maps! thanks again! ...
written 9 weeks ago by junsionglow20
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Comment: C: Very low unique mapped reads - STAR alignment
... thanks!! I will give it a try and keep you updated. Thanks again! ...
written 9 weeks ago by junsionglow20
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Comment: C: Very low unique mapped reads - STAR alignment
... yeah, they do belong to the right GRCh38 assembly... i'm puzzled! ...
written 9 weeks ago by junsionglow20
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Comment: C: Very low unique mapped reads - STAR alignment
... Thanks guys, these fastq files are from published GEO SRA https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3109339 and I obtained the Fastq via fastq-dump. They used GENCODE GRCh38 v26 gene annotation, while I used these to make the index, GCF_000001405.26_GRCh38_genomic.fna GCF_00 ...
written 9 weeks ago by junsionglow20
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Very low unique mapped reads - STAR alignment
... Hi all, while looking at my `log.final.out` file, it dawned on me that my uniquely mapped reads is really low. See below: Mapping speed, Million of reads per hour | 113.33 Number of input reads | 11050047 Average i ...
rna-seq written 9 weeks ago by junsionglow20 • updated 9 weeks ago by h.mon20k
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Comment: C: STAR alignment killed
... Dear Marks and Genomax, Finally gotten it to work. There was 2 part problem, one was my indexing, the other was memory (I believe). So when I submitted a Slurm job requesting for memory, that worked! Thanks guys! ...
written 9 weeks ago by junsionglow20

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