User: Farbod
Farbod • 3.1k
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Hi, I love Biology and Genetics and I have done my PhD thesis on "sturgeon fish RNA-seq" as my MSc was in aquaculture. I am interested in miRNA and epigenetics, too. And having about 4 years of experience in the field of bioinformatics.
Posts by Farbod
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... Hi @genomax, You mean using this genome that is not well-annotated, the genome guided approach is not so much valuable, correct?
of course they have run some [RNA-seq in their genome sequencing][1] project, too (would you please have a look?).
By "since I have trinity assembled transcripts" , can ...
written 10 weeks ago by
Farbod • 3.1k
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... Thank you,
How I can understand that there is any known splice sites information for this "whole genome shotgun sequence" ?
it's structure is as :
chromosome 1
chromosome 2
.
.
chromosome 33
chromosome 34
AND many "unplaced genomic scaffold " ! ...
written 10 weeks ago by
Farbod • 3.1k
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... Dear @lieven.sterck, hi and thanks.
It seems that your idea is different from @genomax,
You believe that as I do not have "the file of known splice sites", I should use the SAM files obtained from my script using "--dta" and proceed to the next level. Correct?
...
written 10 weeks ago by
Farbod • 3.1k
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... Dear @genomax, Hi
I do not have any "file of known splice sites", So in this case you mean I should re-create a new indexed genome using "--ss and --exon" and then map all the reads again using "--dta". yes?
Can we say it is the preferred / standard approach of using HISAT2 for genome-guided? ...
written 10 weeks ago by
Farbod • 3.1k
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... Dear Biostars, Hi,
I have the RNA-seq data of a fish (3 cond1 and 3 cond2 as biological replicates) and I have done **Trinity** de novo assembly and **DEG** analysis on these data. Now the **draft genome** of that species have released. I want to run a **genome-guided** **DEG analysis**, too, to co ...
written 10 weeks ago by
Farbod • 3.1k
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Comment:
C: bam file merge
... Dear genomics Newbie, Hi
Please have a look at [To sort or not to Sort][1]?.
I guess you can first use "`samtools merge`" and then "`samtools sort -o`".
[1]: https://www.biostars.org/p/167064/#167065 ...
written 11 weeks ago by
Farbod • 3.1k
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... Dear @Vijay Lakhujani, Hi and thank you. What do you think about my new script?
./hisat2 -p 6 -x --dta ht2_base_salmon_genome -1 '/RNA_Seq_Data/C1_clean_left.fq' -2 '/RNA_Seq_Data/C1_clean_right.fq' -S '/RNA_Seq_Data/C1.sam' &> C1.sam.info
or I should add "`--ss and --exon`" to it, too ...
written 11 weeks ago by
Farbod • 3.1k
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... Dear Biostars, Hi
I have 6 sam files (3 for cond1 and 3 for cond2) produced from HISAT2 from mapping Hiseq2000 RNA-seq data to a newly released draft genome.
Now I want to use StringTie and then proceed for DEG analysis but in the StringTie [manual][1] it says:
"
> Every spliced read alignmen ...
written 11 weeks ago by
Farbod • 3.1k
• updated
11 weeks ago by
Vijay Lakhujani ♦ 3.0k
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... You are right. Thank you very much.
So, I should now proceed to StringTie level. Yes? ...
written 11 weeks ago by
Farbod • 3.1k
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... Hi @Kevin, Now I have 6 .sam files for my 12 fastq files (3 for cond1 and 3 for cond2), and my final goal is DEG analysis.
Should I use them (6 SAM files) directly in StringTie
or I should merge them to just one file? or maybe use SAMtools/BCFtools before StringTie? ...
written 11 weeks ago by
Farbod • 3.1k
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