User: Farbod

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Farbod3.2k
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Hi, I love Biology and Genetics and I have done my PhD thesis on "sturgeon fish RNA-seq" as my studies was in the field of fisheries and aquaculture. I am interested in miRNA and epigenetics, too.

Posts by Farbod

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News: Misunderstood parameter of NCBI BLAST
... Hi, An interesting paper that I just wanted to share it with Biostars: [Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows][1] [1]: https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty833/5106166?redirectedFrom ...
news alignment blast written 7 weeks ago by Farbod3.2k
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Comment: C: What is the prefered script for HISAT2 genome-guided using draft genome? --dta,
... 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 4 months ago by Farbod3.2k
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Comment: C: What is the prefered script for HISAT2 genome-guided approach? --dta, --ss , --e
... 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 4 months ago by Farbod3.2k
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Comment: C: What is the prefered script for HISAT2 genome-guided approach? --dta, --ss , --e
... 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 4 months ago by Farbod3.2k
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Comment: C: What is the prefered script for HISAT2 genome-guided approach? --dta, --ss , --e
... 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 4 months ago by Farbod3.2k
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What is the prefered script for HISAT2 genome-guided using draft genome? --dta or --exon ?
... 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 ...
genome guided alignment rna-seq hisat2 written 4 months ago by Farbod3.2k
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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 4 months ago by Farbod3.2k
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Comment: C: Adding tag XS to HISAT2 sam files perior to StringTie
... 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 4 months ago by Farbod3.2k
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Adding tag XS to HISAT2 sam files perior to StringTie
... 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 ...
stringtie alignment samtools rna-seq hisat2 written 4 months ago by Farbod3.2k • updated 4 months ago by Vijay Lakhujani3.2k
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Comment: C: Please suggest an appropriate genome-guided transcriptome assembler
... You are right. Thank you very much. So, I should now proceed to StringTie level. Yes? ...
written 4 months ago by Farbod3.2k

Latest awards to Farbod

Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Tools for categorize COG/KOG list
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Collecting Genes with similar GO term
Popular Question 3 months ago, created a question with more than 1,000 views. For Collecting Genes with similar GO term
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Popular Question 3 months ago, created a question with more than 1,000 views. For Collecting Genes with similar GO term
Popular Question 5 months ago, created a question with more than 1,000 views. For Collecting Genes with similar GO term
Popular Question 6 months ago, created a question with more than 1,000 views. For Collecting Genes with similar GO term
Popular Question 6 months ago, created a question with more than 1,000 views. For merging all coordinate-sorted bam files for Trinity genome-guided approach?
Popular Question 6 months ago, created a question with more than 1,000 views. For how to collecting all isoforms of a gene from Trinity.fasta file ?
Popular Question 6 months ago, created a question with more than 1,000 views. For how to map de novo assembly to reference genome ?
Popular Question 6 months ago, created a question with more than 1,000 views. For how to map de novo assembly to reference genome ?
Popular Question 7 months ago, created a question with more than 1,000 views. For how to map de novo assembly to reference genome ?
Popular Question 7 months ago, created a question with more than 1,000 views. For merging all coordinate-sorted bam files for Trinity genome-guided approach?
Popular Question 8 months ago, created a question with more than 1,000 views. For how to map de novo assembly to reference genome ?
Popular Question 8 months ago, created a question with more than 1,000 views. For showing row names and dendrogram in same side, using heatmap() or pheatmap()
Popular Question 11 months ago, created a question with more than 1,000 views. For DIAMOND blast imported into MEGAN6 has no taxonomic assignment
Teacher 11 months ago, created an answer with at least 3 up-votes. For C: Can't open gz file
Student 17 months ago, asked a question with at least 3 up-votes. For DIAMOND blast imported into MEGAN6 has no taxonomic assignment
Scholar 20 months ago, created an answer that has been accepted. For A: mireap procedure short tutorial
Appreciated 21 months ago, created a post with more than 5 votes. For A: Tools for categorize COG/KOG list

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