User: lkianmehr
lkianmehr • 30
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Posts by lkianmehr
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... Hello,
short read sequence alignment of RNA-seq in Bam format are visulaized using IGV, something is wrong I think, technical replicates of each sample are not exactly same, I mean coverage track of them is not identical even with same data range. Do you know it should be same? or is it normal?
th ...
written 7 weeks ago by
lkianmehr • 30
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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 7 months ago by
lkianmehr • 30
• updated
7 months ago by
lakhujanivijay ♦ 4.5k
2
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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 7 months ago by
lkianmehr • 30
• updated
7 months ago by
shenwei356 ♦ 4.8k
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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 9 months ago by
lkianmehr • 30
1
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1
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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 9 months ago by
lkianmehr • 30
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1
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... geneSCF-master-source-v1.1-p2 ...
written 9 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 9 months ago by
lkianmehr • 30
2
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370
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1
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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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