User: Boboboe

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Boboboe10
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Posts by Boboboe

<prev • 8 results • page 1 of 1 • next >
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Comment: C: GEO .cel file and the preview table are they the same thing?
... Thank you so much for your quick response! I just can't quite figure out how to download that table from that page :( view full table just show me the table in another page in HTML format and when I try to download it by using "save as" it's still in form of html. How do I download the table? ** ed ...
written 7 days ago by Boboboe10
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GEO .cel file and the preview table are they the same thing?
... Dear all, I'm trying to use this data for differential expression analysis. I would like to use the processed data, which seems like it is the .cel file at the supplementary file. On top of that, there's also a data table shown. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM496105 I just ...
geo microarray rna-seq written 8 days ago by Boboboe10 • updated 8 days ago by Ahill1.3k
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Comment: C: STAR RNA-seq aligned output ReadsPerGene.out.tab
... I used gencode annotation. and when I looked into the gene_id, all the id are in form of "ENSG00000223972.5_2", with an underscore and a number attached to it. what is the number after the underscore? is it the exon? (e.g for my example, it would be the exon 2 of ENSG00000223972.5 gene). If that's ...
written 6 weeks ago by Boboboe10
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Comment: C: STAR RNA-seq aligned output ReadsPerGene.out.tab
... Thank you for your response. I am pretty sure my data is unstranded. in that case, should I use the second column of the output for the analysis? ...
written 7 weeks ago by Boboboe10
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STAR RNA-seq aligned output ReadsPerGene.out.tab
... Hi, I'm trying to perform differential expression analysis on different conditions my RNA-seq data. I used --quant GeneCount(something similar, forgot the except option) to get the output ReadsPerGene.out.tab. I was wondering if I could use the read count from ReadsPerGene table generated from STA ...
star differential expression analysis rna-seq written 7 weeks ago by Boboboe10 • updated 7 weeks ago by h.mon21k
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Ensembl bacterial genome alignment - use top level or chromosome?
... Hi all, I'm trying to align my sequecing data to a whole genus of bacteria. There are multiple files for each bacteria - there are chromosome, top level, and non-chromosomal.(an example of what I'm looking at:ftp://ftp.ensemblgenomes.org/pub/bacteria/release-40/fasta/bacteria_0_collection/mycobacte ...
ensembl alignment chip-seq bacteria chromosome written 10 weeks ago by Boboboe10 • updated 10 weeks ago by Emily_Ensembl16k
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Is subtelomeric region and pericentromeric region defined in human genome?
... I've been trying to see if there's any coordinates for these but doesn't have much luck. Saw a bunch of people defining it by +-2MB around the centromere gap and 30kb away from the telomere. I was wondering if you guys have any knowledge about this. Thanks! ...
genome human pericentromeric subtelomeric written 15 months ago by Boboboe10 • updated 15 months ago by Jean-Karim Heriche17k
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Chip seq control library prep?
... Hello everyone, I recently started learning more about sequencing and I'm a little confused about data formats and also how you prepare your input. From my understanding, input is to let you know what the reads would be if you are not enriching for reads that are interacting with your target protei ...
sequencing alignment chip-seq aquas written 15 months ago by Boboboe10 • updated 15 months ago by Kevin Blighe33k

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