User: bioinfo17

gravatar for bioinfo17
bioinfo1730
Reputation:
30
Status:
New User
Location:
Last seen:
1 week, 5 days ago
Joined:
3 years, 6 months ago
Email:
p*******@yahoo.co.uk

Posts by bioinfo17

<prev • 30 results • page 1 of 3 • next >
1
vote
1
answer
528
views
1
answers
Answer: A: how to identify cores, accesory and unique sequences from proteomes
... use the -singles option in proteinortho command ...
written 19 months ago by bioinfo1730
0
votes
8
answers
4.2k
views
8
answers
Answer: A: Edgeredef Failed When Running Repeatmodeler
... Encountered the same problem: RepeatModeler version open-1.0.11 RECON 1.05 > Comparison Time: 00:00:16 (hh:mm:ss) Elapsed Time, 901 HSPs Collected > - RECON: Running imagespread.. RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time > - RECON: Running initial definition of eleme ...
written 20 months ago by bioinfo1730
0
votes
1
answer
3.7k
views
1
answers
Comment: C: hisat2 parameters for paired end and single end reads from same samples
... Estimation of the insert size is a great idea. I will follow that. > Stringtie counts the number of reads that cover each position I have read the manual of stringtie but couldn't find an answer if it assembles transcripts based on both paired end and singletons reads and the counts generated w ...
written 2.5 years ago by bioinfo1730
3
votes
1
answer
3.7k
views
1
answer
hisat2 parameters for paired end and single end reads from same samples
... Hi, I have paired end R1.fastq, R2.fastq and singletons.fastq files for the same samples. What parameters should I use for aligning reads against a genome of interest? 1) hisat2 -1 R1.fastq, -2 R2.fastq, -U singletons.fastq or just treat all the files as unpaired and use 2) hisat2 -U R1.fastq, ...
hisat stringtie alignment rna-seq hisat2 written 2.5 years ago by bioinfo1730 • updated 2.5 years ago by Macspider3.0k
0
votes
1
answer
1.2k
views
1
answers
Comment: C: GMAP v2017-06-20 error
... Thanks, will do that. ...
written 2.7 years ago by bioinfo1730
0
votes
1
answer
1.2k
views
1
answer
GMAP v2017-06-20 error
... Hi all, I am trying to align the de novo transcriptome (transcripts) against the reference genome via GMAP using the following command below: 1) have build a database of the genome using gmap-build command, 2) gmapl -D . -d database -2 genome_fasta trinity_fasta -f samse > trinity_gmap. ...
software error gmap alignment written 2.7 years ago by bioinfo1730 • updated 2.4 years ago by KVC_bioinfo410
0
votes
2
answers
1.8k
views
2
answers
Comment: C: Aligning reads to genome together with transcriptome
... Hi EVR, What approach did you finally use for your analysis, would be really good to share? Thanks ...
written 2.7 years ago by bioinfo1730
0
votes
1
answer
1.6k
views
1
answers
Comment: C: Hisat2 build index for genome + transcriptome files together
... Will give Salmon a try, thank you! ...
written 2.7 years ago by bioinfo1730
0
votes
1
answer
1.6k
views
1
answers
Comment: C: Hisat2 build index for genome + transcriptome files together
... Thanks Devon for your quick reply. The % alignment rate was very low (~2-20%) when the sample reads were mapped against the individual genome fasta file, however, the alignment % significantly increased (~60-80%) when the sample reads were mapped against the transcriptome alone. I am unsure which on ...
written 2.7 years ago by bioinfo1730
1
vote
1
answer
1.6k
views
1
answer
Hisat2 build index for genome + transcriptome files together
... Hi, Could anyone please explain how to use Hisat2 when both the genome and transcriptome is available for the same reference strain. The genome is annoated using maker and hence have the gene models in gff format. The transcriptome is also available but is present only as an assembled fasta format. ...
rna-seq written 2.7 years ago by bioinfo1730 • updated 2.7 years ago by Devon Ryan94k

Latest awards to bioinfo17

Popular Question 3 months ago, created a question with more than 1,000 views. For hisat2 parameters for paired end and single end reads from same samples
Popular Question 9 months ago, created a question with more than 1,000 views. For Hisat2 build index for genome + transcriptome files together
Popular Question 17 months ago, created a question with more than 1,000 views. For Augustus scipio error
Popular Question 18 months ago, created a question with more than 1,000 views. For Augustus scipio error
Popular Question 2.1 years ago, created a question with more than 1,000 views. For hisat2 parameters for paired end and single end reads from same samples

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1855 users visited in the last hour