User: lkianmehr
lkianmehr • 30
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Posts by lkianmehr
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... I have got the result like below, what does it mean? contaminants determine the number of reads including that specific sequence or something else?
Input: 65975862 reads 6554014910 bases.
Contaminants: 195232 reads (0.30%) 19519262 bases (0.30%)
Total Rem ...
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... I just want to know how many of these specific sequence are there in these paired-read sequence to get proportion of that between all? I have tried by
bbduk.sh in1=D1_L001_1.fastq.gz in2=D1_L001_2 out=D1.fq literal=TAACCCTAACCCTAACCCTAACCC k=24 mm=f int=f
but this command just extract all re ...
written 3 months ago by
lkianmehr • 30
• updated
3 months ago by
Vijay Lakhujani ♦ 4.1k
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... Hello,
Do you have any idea about How to get proportion of specific sequence (defined as a separate fastq file=
```
@1
TAACCCTAACCCTAACCCTAACCC
+
JJJJJJJJJJJJJJJJJJJJJJJJ
@2
TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC
+
JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ
```
) in several paired- ...
written 3 months ago by
lkianmehr • 30
• updated
3 months ago by
shenwei356 ♦ 4.7k
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... could you please make some example of those specialized databases annotate gene ontology or functional terms from lncRNAs as well and which stage you recommend to separate protein_codings before DGE analysis or doesn't matter if done after that? ...
written 5 months ago by
lkianmehr • 30
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... I have a list of transcripts (quantified by Salmon), may I filtered them out based on biotype, for instance, protein_codings or lncRNA, then do GO for each one separately? ...
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... I have got transcript quantification by Salmon, then import them to tximport and got transcript count, length and abundances. now I would like to make a transcript coverage graph in terms of normalized counts on normalized position along transcript. I have normalized counts by DESeq2 but I don't kno ...
written 5 months ago by
lkianmehr • 30
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... geneSCF-master-source-v1.1-p2 ...
written 5 months ago by
lkianmehr • 30
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I have tried to do GO with genescf as I did for the same gene symbols list by DAVID, but results with genescf are very different, and no P-values is significant (based on EASE less than 0.05). need to mention that I have used mgi as -db. DO you have any idea about this conflict? ...
written 5 months ago by
lkianmehr • 30
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... Hello,
I have a list of MOUSE genes (from RNA-seq analysis) include 800 up and 7150 down regulated from DESeq2 . I did GO enrichment analysis for up-regulated genes by DAVID, and got 3 list of functional groups (84 GO term for Molecular function, 57 GO term for cellular component and 163 Go term f ...
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... I have run that command on two fastq files that are sequenced on the same library, I got one value = 0.119817, what does it mean? it means they have just 0.1 percent difference? ...
written 6 months ago by
lkianmehr • 30
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