User: Adeler001

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Adeler0010
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Posts by Adeler001

<prev • 27 results • page 1 of 3 • next >
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What is the best approach to normalize exon read counts between samples ?
... Hello I'm trying to calculate the read count for each exon in one of my genes for 3 affected patients and 3 unaffected patients from my RNA-seq data . I'm trying to find the best way to normalize these read counts to factor in variance in exon read depth and exon length between patients. Would calcu ...
rna-seq written 7 months ago by Adeler0010
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Comment: C: searching for specific RNA nucleotide sequences
... thanks for the reply . is there a way to a call sequence that has a specific nucleotide pattern for most reads but may alter in this pattern by 3 or 5 nucleotide for other reads? ...
written 8 months ago by Adeler0010
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searching for specific RNA nucleotide sequences
... I have a unique chimera RNA nucleotide sequence. Is there a script I can use to to search my RNA seq bam files for that specific nucleotide motif. ...
rna-seq written 8 months ago by Adeler0010 • updated 8 months ago by wm490
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Comment: C: issues using Value Matching command in R
... here is what my table looks like Geneid Chr Start end Strand Length D4001 D4002 D4003 D4004 D4005 D4006 ENSG00000223972.4 chr1 11869 12227 + 35 8 22 33 44 ...
written 10 months ago by Adeler0010
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Comment: C: issues using Value Matching command in R
... Geneid is one of the column headers of my table. I didn't think of using the `read.csv` command. i didn't install any packages . i just tried the `read.csv` command and i get this error message : Error in read.table(file = file, header = header, sep = sep, quote = quote, : more columns than c ...
written 10 months ago by Adeler0010
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issues using Value Matching command in R
... Hello I am trying to use the Value Matching command in R to find a specific ensemble exon code in my exon count table generated by featurecounts for my RNAseq data . Everything works until I used the `%in%` command. Here is the script I used: tab= read.table("exons_RNA-seq_sorted.csv", heade ...
R rna-seq written 10 months ago by Adeler0010
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Comment: A: RNAseq read counts generated by FeatureCounts
... ok thank you for your replies genomax and kevin ...
written 11 months ago by Adeler0010
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Comment: A: do not sort option on featurecounts
... OK thank you AT point and genomax for your responses . I really appreciate it ...
written 11 months ago by Adeler0010
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Comment: C: do not sort option on featurecounts
... Hello ATpoint and genomax thank you for your response, the reason I wanted to add the `--donotsort` option is that I was afraid that the feature counts program would not be able to properly account for paired reads that are not close in proximity due to being a part of a duplication or deletion ...
written 11 months ago by Adeler0010
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Comment: C: do not sort option on featurecounts
... thanks for answering my question , I used -p and −−donotsort together in the same command line. Would adding -p cancel out the do not sort? since you said that by adding paired-end counting (-p) it will by default sort the BAM files prior to quantification. here's my script below cd /h ...
written 11 months ago by Adeler0010 • updated 11 months ago by ATpoint42k

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