User: abhijit.synl

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abhijit.synl50
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Posts by abhijit.synl

<prev • 17 results • page 1 of 2 • next >
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Comment: A: Adding CDS features to Gff3 file
... Please attach a sample of your Gff3 file. Maybe the first 250 lines. ...
written 8 weeks ago by abhijit.synl50
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Answer: A: Adding CDS features to Gff3 file
... You will need to install the following and make sure they are in your PATH variable 1) Gffread utility 2) Genometools 3) GAAS Toolkit a) Tidy your GFF3 gffread -C -F -T --no-pseudo -o FOO1".gtf" FOO.gff3 gt gtf_to_gff3 -tidy -force -o FOO".gff3" FOO1".gtf" (gt = GenomeTools executable) ...
written 8 weeks ago by abhijit.synl50
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Comment: A: Ncbi-Blast+ Version 2.2.23 'Make' Error
... Hello, Sorry to be reopening this thread after 7 years! But I am facing issues trying to install rpsblast and rpsproc for interproscan 5. I have followed the instructions around "Compiling Binaries" in the Interproscan handbook for rpsblast and rpsproc. I am able to get to the configure step, but m ...
written 9 weeks ago by abhijit.synl50
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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 4 months 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 4 months ago by abhijit.synl50 • updated 4 months ago by lakhujanivijay4.4k
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Comment: A: Adding CDS features to Gff3 file
... This is resolved. please close thread ...
written 4 months ago by abhijit.synl50
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Comment: C: Adding CDS features to Gff3 file
... Though not directly but can be acheived using a combination of Genometools and PASA ...
written 4 months 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 5 months 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 11 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 11 months ago by abhijit.synl50

Latest awards to abhijit.synl

Popular Question 4 months ago, created a question with more than 1,000 views. For Getting the protein Domain architecture from a domtblout
Scholar 4 months ago, created an answer that has been accepted. For C: Adding CDS features to Gff3 file
Student 24 months ago, asked a question with at least 3 up-votes. For Getting the protein Domain architecture from a domtblout
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Getting the protein Domain architecture from a domtblout

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