User: abhijit.synl

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abhijit.synl50
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United States
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Posts by abhijit.synl

<prev • 14 results • page 1 of 2 • next >
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Comment: A: Merging Bam Files
... I have a question related to merging of bam files. Please see the attached image to understand my question. I have SE reads coming from separate samples mapped to the same genome using HISAT2. Thus I have separate bam files. I am merging them using the following command samtools merge -h in-1.b ...
written 5 days ago by abhijit.synl50
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Spaln usage after repeatmasking
... Hello All, I was wondering if anyone has used the Spaln program (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488211/ and http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/) to map and align cDNA and EST sequences to the genome. I am particularly interested in understanding the Spaln behaviour ...
genome mapping genome annotation genome alignment written 22 days ago by abhijit.synl50 • updated 22 days ago by Vijay Lakhujani4.1k
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Comment: A: Adding CDS features to Gff3 file
... This is resolved. please close thread ...
written 22 days ago by abhijit.synl50
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Answer: C: Adding CDS features to Gff3 file
... Though not directly but can be acheived using a combination of Genometools and PASA ...
written 22 days ago by abhijit.synl50
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Get publication counts per gene per year
... Hi I would like to write a edirect query to extract number of publications per gene per year. The group I am interested in is Viridiplantae. So for all species under this group, given a date range, I would like to get the publication count for each gene in that species. The final output that I am l ...
bioinformatics eutilities written 8 weeks ago by abhijit.synl50
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Comment: C: Sam file manipulation
... I want to use the program TransComb. It needs Tophat2 output with the Hit Query index field. Hisat2 does not give that. Here is the output. I am masking the reads cuz data is proprietary 34768728/1 256 N1 29379 1 50M * 0 0 NNNNNNNNNNNNNNNNNNNNNNNNNNNN ...
written 7 months ago by abhijit.synl50
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Sam file manipulation
... Hello All, I have a standard SAM output from the HISAT2 splice aware aligner. I want to add the Query hit index tag to the output, which indicates position of the alignment record in SAM file. Is there a way to do that? The dataset is 50 bp SE RNA-Seq reads mapped to the genome using HISAT2 Thank ...
rna-seq format manipulation written 7 months ago by abhijit.synl50
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Adding CDS features to Gff3 file
... Hello, I would like to add the CDS feature to my Gff3 file, that has exons in it. I saw that genometools can do this for you > gt cds -startcodon -finalstopcodon -seqfile foo.fasta -o foo.gff3 [GFF3-FILE] I am looking for the CDS to be the longest ORF with an ATG start codon per mRNA. Will the ...
genome annotation bioinformatics written 17 months ago by abhijit.synl50
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Genome repeat masking before gene annotation
... Hello All, I wanted to know whether repeatmasking a genome or genome fragment, before performing gene annotation, is a good idea. The literature (http://www.nature.com/nrg/journal/v1...l/nrg3174.html, http://onlinelibrary.wiley.com/doi/1...eva.12178/full) and software such as MAKER, and PASA advoca ...
genome annotation bioinformatics written 20 months ago by abhijit.synl50
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BAC annotation strategy
... Hello All, I have a strategy question related to BAC annotation. I have 500 BAC sequences from a single maize line to annotate. I am faced with a strategy dilemma. 1) Put all the BAC sequences in one file, create a multi-fasta file and run the annotation. 2) Go about the annotation on a per BAC ...
sequence annotation bac written 2.3 years ago by abhijit.synl50 • updated 2.3 years ago by WouterDeCoster39k

Latest awards to abhijit.synl

Popular Question 2 days ago, created a question with more than 1,000 views. For Getting the protein Domain architecture from a domtblout
Scholar 22 days ago, created an answer that has been accepted. For C: Adding CDS features to Gff3 file
Student 20 months ago, asked a question with at least 3 up-votes. For Getting the protein Domain architecture from a domtblout
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Getting the protein Domain architecture from a domtblout

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