User: liorglic

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liorglic50
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Posts by liorglic

<prev • 18 results • page 1 of 2 • next >
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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 27 days 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 4 weeks 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 7 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 7 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 7 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 8 months ago by liorglic50 • updated 8 months ago by Carlo Yague4.4k
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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 9 months ago by liorglic50
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Comment: C: RNA-seq data for de-novo transcript assembly
... No, not particularly... ...
written 11 months ago by liorglic50
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Comment: C: RNA-seq data for de-novo transcript assembly
... Yes, if I look at other varieties/cultivars other than the one used to produce the reference (Heinz). This had not yet been done in tomato, but in other organisms (e.g rice and maize) non-reference cultivars showed a substantial amount of novel genes not found in the reference. ...
written 11 months ago by liorglic50
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Comment: C: RNA-seq data for de-novo transcript assembly
... Thank you. This is very helpful. As I said, I'm not planning on producing new RNA-seq data right now, but rather use data available from various DBs. So for example I found a data set comprised of ~2.8Gb sequencing data, with reads of length 61. Would you consider assembling this or would you say ...
written 11 months ago by liorglic50

Latest awards to liorglic

Scholar 27 days ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Popular Question 11 months ago, created a question with more than 1,000 views. For Where can I find a small NGS raw data set?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Pysam (python) problem parsing BAM reference id

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