User: liorglic

gravatar for liorglic
liorglic40
Reputation:
40
Status:
New User
Location:
Last seen:
12 hours ago
Joined:
2 years, 2 months ago
Email:
l*******@mail.tau.ac.il

Posts by liorglic

<prev • 13 results • page 1 of 2 • next >
0
votes
1
answer
98
views
1
answer
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 9 days ago by liorglic40 • updated 9 days ago by Carlo Yague4.0k
0
votes
0
answers
88
views
0
answers
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 6 weeks ago by liorglic40
0
votes
1
answer
287
views
1
answers
Comment: C: RNA-seq data for de-novo transcript assembly
... No, not particularly... ...
written 3 months ago by liorglic40
0
votes
1
answer
287
views
1
answers
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 3 months ago by liorglic40
0
votes
1
answer
287
views
1
answers
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 3 months ago by liorglic40
3
votes
1
answer
287
views
5 follow
1
answer
RNA-seq data for de-novo transcript assembly
... Hello, I'm rather new to RNA-seq analysis and more familiar with DNA sequencing. I'd like to perform de-novo assembly of transcripts from publicly-available (i.e published) RNA-seq data in tomato and its wild relative. the reasons I need to do that are: a. I want to discover novel genes not pr ...
assembly rna rna-seq written 3 months ago by liorglic40 • updated 3 months ago by lieven.sterck1.6k
0
votes
1
answer
199
views
1
answers
Comment: C: Strategy for genome annotation for a new individual of a well-established specie
... Thanks, I wasn't familiar with this software. However, since I'm also interested in detecting new genes not present in the reference annotation, I'd like to use the transcriptomic data on top of that, and this is where most of the noise comes from. ...
written 3 months ago by liorglic40
1
vote
1
answer
199
views
5 follow
1
answer
Strategy for genome annotation for a new individual of a well-established species
... Hi, I am new to the topic of genome annotation and would like to get some advice regarding my planned strategy. So, I am exploring genetic diversity in maize, in for this purpose I have de-novo assembled a genome of a variant which is supposed to be quite diverse from the reference. I'd now like ...
assembly annotation transcriptome written 3 months ago by liorglic40 • updated 3 months ago by Rohit1.3k
2
votes
2
answers
364
views
5 follow
2
answers
Gene copies vs. gene paralogs - what's the difference
... Hi all, I'm trying to get into the theory and practice of gene copy number variation (CNV) analysis, but there is something basic confusing me, which I couldn't yet figure out. Sorry if this is a dumb/trivial question - would appreciate your help anyway. My confusion is regarding the terms 'gene c ...
wgs cnv paralogs written 5 months ago by liorglic40 • updated 5 months ago by Emily_Ensembl15k
1
vote
1
answer
713
views
1
answer
Genome annotation tools - current status. Machine learning?
... Hi there, I am getting started with learning genome annotation. After reading a few (somewhat theoretical) review papers, I thought it'd be nice to hear from the community of the current status of genome annotation tools. Could you please list some tools currently in frequent use? If you know of ...
genome assembly machine learning annotation written 18 months ago by liorglic40 • updated 18 months ago by prash10

Latest awards to liorglic

Popular Question 3 months ago, created a question with more than 1,000 views. For Where can I find a small NGS raw data set?
Popular Question 17 months ago, created a question with more than 1,000 views. For Pysam (python) problem parsing BAM reference id

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1588 users visited in the last hour