User: liorglic

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liorglic50
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Posts by liorglic

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Comment: C: Reference-guided assembly from short reads
... Thanks, I've seen these posts, but this still doesn't answer my question, so I'd still like to get some more relevant and up-to-date advise if anyone has one. ...
written 10 weeks ago by liorglic50
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Reference-guided assembly from short reads
... Hello, I have short reads (Illumina) data with x30-40 depth for several varieties of a plant genome. A reference genome for the same species exists. I would like to assemble the reads into pseudomolecules based on the reference genome. Is anybody aware of an existing tool that can do that? ...
assembly ngs written 10 weeks ago by liorglic50
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Answer: A: What's the right way to submit a genome assembly to NCBI?
... I ended up contacting NCBI help desk (as suggested by @genomax). Here's the answer I got: > We recommend you to submit the gapped scaffold fasta file and answer > the gap questions on the submission portal, along with the agp file > that includes the chromosomes and the unplaced scaffold ...
written 6 months ago by liorglic50
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What's the right way to submit a genome assembly to NCBI?
... Hi everybody, I'd like to submit an eukaryotic assembly to NCBI. I've gone through the [Genome submission guide][1], but am still not clear on what's exactly expected and would like some advice from someone who did this lately. I have all three levels of the assembly: contigs, scaffolds and chromo ...
assembly written 6 months ago by liorglic50
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Comment: C: Merging multiple sets of transcripts (generated by Trinity)
... Thanks I understand now. I decided to try a wrapper tool called DRAP (https://peerj.com/articles/2988/) which has a module called runMeta. It uses CD-HIT-EST to collapse transcripts and the assembler TGICL to elongate transcripts. I'll see how this works for me. ...
written 12 months ago by liorglic50
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Comment: C: Merging multiple sets of transcripts (generated by Trinity)
... Thanks @mks002. I am familiar with CD-HIT, and have seen it mentioned in this context before, but I still don't understand how it can solve my problem. CD-HIT clusters transcripts based on a similarity threshold. How can such output be used to actually merge transcripts together? Can you explain in ...
written 12 months ago by liorglic50
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Merging multiple sets of transcripts (generated by Trinity)
... Hi everyone. Need your advice on an issue I'm having. So, I have used Trinity in order to create transcriptome assemblies from ~30 data sets of RNA-Seq, downloaded from SRA. All data sets come from the same species (tomato), but from different variants, conditions and tissues. My aim is to produce ...
assembly rna-seq written 12 months ago by liorglic50
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extract one-side unmapped reads from sam
... Hello, I've ran [TopHat][1] and aligned paired end (PE) reads to a reference genome. TopHat outputs two bam files: accepted_hits.bam and unmapped.bam. I'd like to extract from unmapped.bam only those reads where only one side of the pair (R1 or R2) was not mapped, i.e. exclude records where bo ...
tophat bam samtools sam written 13 months ago by liorglic50 • updated 13 months ago by Carlo Yague4.6k
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cDNA/EST/Random library selection for transcriptome assembly
... Hi I am collecting RNA-Seq data from NCBI SRA for a specific organism, in order to create a de-novo transcriptome assembly. For each data set archived in SRA, the "Library Selection" field is given, usually indicating either "cDNA", "EST" or "RANDOM". According to [this page][1], the definitions ...
assembly cdna est rna-seq sequencing written 14 months ago by liorglic50
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Comment: C: RNA-seq data for de-novo transcript assembly
... No, not particularly... ...
written 16 months ago by liorglic50

Latest awards to liorglic

Scholar 6 months ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Popular Question 16 months ago, created a question with more than 1,000 views. For Where can I find a small NGS raw data set?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Pysam (python) problem parsing BAM reference id

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