User: lkianmehr
lkianmehr • 50
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- 9 hours ago
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- 2 years, 8 months ago
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Posts by lkianmehr
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... I need to calculate the percentage of a repetitive motif (TTAGGG/CCCTAA) in my RNA-seq data (Fastq files). I used BBDUK (this command :
bbduk.sh in1=R3_L002_1.fastq.gz in2=R3_L002_2.fastq.gz literal=TAACCCTAACCCTAACCCTAACCC k=24 mm=f int=f).
below is an output that I've got.
D1_L001:
...
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... I have some questions:
1- can I seek for tRNA-derived fragments or generally small coding and non-coding RNA on RNA-seq data?
2- if so, is Salmon useful for this purpose?
thank you ...
written 10 months ago by
lkianmehr • 50
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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 17 months ago by
lkianmehr • 50
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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 23 months ago by
lkianmehr • 50
• updated
23 months ago by
lakhujanivijay ♦ 5.3k
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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 23 months ago by
lkianmehr • 50
• updated
23 months ago by
shenwei356 ♦ 5.7k
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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 2.0 years ago by
lkianmehr • 50
1
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1
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700
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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 2.0 years ago by
lkianmehr • 50
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1
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34k
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... geneSCF-master-source-v1.1-p2 ...
written 2.0 years ago by
lkianmehr • 50
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