User: dovah

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dovah30
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Posts by dovah

<prev • 16 results • page 1 of 2 • next >
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Answer: A: PASA pipeline: just compare to the reference annotation
... Answer from the authors: > PASA ends up using gff3 format instead of sam format for uploading the > alignments. If somebody has the gmap gff3 output, then can be done to > just upload that directly using the custom alignment importer, but not > with sam. They suggest just having PASA r ...
written 17 months ago by dovah30
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PASA pipeline: just compare to the reference annotation
... Hello, I would like to ask if anyone has experience in running a subset of the PASA pipeline, in particular for the reconciliation of some experimental 'transcripts' with the reference annotation. In more detail, I am working with RNA-seq data from D. melanogaster. I have reconstructed the 'transc ...
trinity pasa isoforms rna-seq transcripts written 17 months ago by dovah30
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transcriptome assembly evaluation
... Hi all. I would like to compare a de-novo (Trinity) and a reference-based (Cufflinks) Illumina assembly, done on the same dataset (organism D. melanogaster). You know how should I proceed? I am particularly interested in detecting splice variants. Many thanks! ...
assembly transcriptome written 2.2 years ago by dovah30 • updated 22 months ago by BioBing100
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Comment: C: vcf to xls wrong columns
... A text editor would be more apporpriate. What OS are you working on? ...
written 2.4 years ago by dovah30
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Comment: C: vcf to xls wrong columns
... @ cristina_sabiers : is there a specific reason why you have to do it in excel? ...
written 2.4 years ago by dovah30
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Comment: C: GTEx genotype data
... For someone who is not familiar with GTEx data this question is totally unclear. could you please specify: - where is the information about the genotype in your file? - what you define as genotype matrix? I think your problem can be easily solved by a grep/sed by the way. Also, beware of postin ...
written 2.4 years ago by dovah30
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Comment: C: running Cufflinks with input from HIsat2
... I tried with and without sorting (if by that you mean, samtools sort). My command was: `cufflinks --GTF-guide Drosophila_melanogaster.BDGP6.84.gtf --library-type fr-firststrand hisat2_alignment.sam` If I do not sort the input file, then I got the error: You are using Cufflinks v2.2.1, which i ...
written 2.4 years ago by dovah30
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Comment: C: running Cufflinks with input from HIsat2
... Hi! I have 251929648 reads (x2 because of paired-end). I am using Cufflinks for reference-based transcriptome assembly starting from RNA-seq reads, which are aligned back to reference genome, and currently in sam/bam format. The genome has been indexed using reference gtf file. In parallel I am als ...
written 2.4 years ago by dovah30
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running Cufflinks with input from HIsat2
... Hi all, I read on Cufflinks man page that input sam file, coming from others mappers than TopHat, must be sorted this way: sort -k 3,3 -k 4,4n hits.sam > hits.sam.sorted However, it is taking ages, and eventually causes the server on which we are doing calculations to crash. Is there any p ...
transcriptome assembly alignment cufflinks hisat2 written 2.4 years ago by dovah30
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Comment: C: Paired End Trimmomatic producing asymmetric paired read files.
... @Biogeek could you please provide the reference for your usage of keepbothreads ( ":TRUE") and HEADCLIP:10? I cannot find these options on manual, at: http://www.usadellab.org/cms/?page=trimmomatic ...
written 2.4 years ago by dovah30

Latest awards to dovah

Popular Question 13 months ago, created a question with more than 1,000 views. For Parsing uniprot gene names to get the correspondng entry names
Popular Question 13 months ago, created a question with more than 1,000 views. For running Cufflinks with input from HIsat2
Popular Question 14 months ago, created a question with more than 1,000 views. For Parsing uniprot gene names to get the correspondng entry names
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Parsing uniprot gene names to get the correspondng entry names
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Hisat2 on multiple paired-end input

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