User: utsafar

gravatar for utsafar
utsafar70
Reputation:
70
Status:
Trusted
Location:
Last seen:
2 weeks ago
Joined:
4 years, 5 months ago
Email:
u******@gmail.com

Posts by utsafar

<prev • 37 results • page 1 of 4 • next >
0
votes
0
answers
144
views
0
answers
Comment: C: Why are some mapped reads not mapped completely?
... Let me ask another question. Using FreeBayes I want to obtain coverage of both reference varinat and alternative variant in each variation position of each ORF (and do some more things with this coverage numbers). In every ORF, I checked coverage mean, standard variation and coefficient of variation ...
written 23 days ago by utsafar70
0
votes
0
answers
144
views
0
answers
Comment: C: Why are some mapped reads not mapped completely?
... I checked in IGB. The soft-clipped parts of reads are not mapped because their sequence is different with reference. In about 30 percent of reads, first 20 to 40 bp and/or last 20 to 40, with different sequences, are soft-clipped. What I have to do now? ...
written 23 days ago by utsafar70
0
votes
0
answers
144
views
0
answers
Comment: C: Why some mapped reads are are not mapped completely?
... It is a shame that I didn't know soft-clipping. Just read about it and watched the CIGAR column data in my bam file. Many reads are soft-clipped. Now what I have to do? Is this mapping trust able at all? ![enter image description here][1] [1]: https://img.techpowerup.org/201110/screenshot-2020- ...
written 24 days ago by utsafar70
0
votes
0
answers
144
views
0
answers
Comment: C: Why some mapped reads are are not mapped completely?
... I used Trinity, get-orf and BWA-MEM in usegalaxy.eu and default options in my work. The quality of data is OK (fastQC). Aligner soft-clip even above 90 percent of reads. I am confused! ...
written 24 days ago by utsafar70
0
votes
0
answers
144
views
0
answers
Comment: C: Why some mapped reads are are not mapped completely?
... I am aware of UTRs and omitted them consciously. Also in my species median protein length is 800 na (2400 bp) so I think looking for Orfs with length 1200 bp and above is fare. I expect, at least in middle of my ORFs, reads map completely. But nested reads (if I use this word correctly) are every w ...
written 24 days ago by utsafar70
14
votes
0
answers
144
views
0
answers
Why are some mapped reads not mapped completely?
... In my work I generated contigs using Trinity, then extracted ORFs (min length 1200 bp) using get-orf, and then mapped RNA-Seq reads to these ORFs. While all reads are 101 bp length, when I watched mapping results using Integrated genome browser I see that mapped length of many reads are below 101 ( ...
mapping rna-seq written 24 days ago by utsafar70 • updated 24 days ago by lieven.sterck9.1k
0
votes
0
answers
120
views
0
answers
How to include depth of coverage of k prior and posterior neighbours of a position in vcf file?
... I used FreeBayes to call variants from BAM file and the reference genome is contigs of RNA-Seq. I have depth of coverage of each variation position. I want to use depth of k (3, 4, 5...) prior and posterior neighbor positions of each variant position to normalize depth of that variant position using ...
vcf sequence rna-seq depth of coverage written 28 days ago by utsafar70
3
votes
2
answers
106
views
2
answers
Answer: C: transfer data from cluster to cluster
... Did you checked this: https://unix.stackexchange.com/questions/106480/how-to-copy-files-from-one-machine-to-another-using-ssh ...
written 4 weeks ago by utsafar70
4
votes
4
answers
309
views
6 follow
4
answers
RNA-Seq differential gene expression without biological and technical replicates.
... What I have is six RNA-Seq datasets from three developmental stages in two conditions (control and treatment), without biological and technical replicates. (I did all the following in usegalaxy.eu) Each dataset was mapped to reference genes using tophat. htseq-count was used to count aligned reads. ...
rna-seq written 4 months ago by utsafar70 • updated 4 months ago by a4106387580
0
votes
2
answers
1.1k
views
2
answers
Comment: C: How can I download data from plants.ensembl.org using wget in biomart?
... Mike and Astrid, thanks to your helps I found my mistakes: This is my wrong command: wget -O result.txt 'http://www.plants.ensembl.org/biomart/martview/martservice?query=' First mistake: I forgot to remove 'www.' from my url 2nd mistake: '/martview' will be removed So this is the example co ...
written 22 months ago by utsafar70

Latest awards to utsafar

Scholar 4 weeks ago, created an answer that has been accepted. For C: transfer data from cluster to cluster
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: transfer data from cluster to cluster
Popular Question 4 months ago, created a question with more than 1,000 views. For Are transcription factors some kind of eQTLs?
Popular Question 4 months ago, created a question with more than 1,000 views. For Three questions about an RNA-seq and protein domains data analysis.
Supporter 4 months ago, voted at least 25 times.
Popular Question 14 months ago, created a question with more than 1,000 views. For plant housekeeping genes without paralogs
Popular Question 14 months ago, created a question with more than 1,000 views. For identity, positivity and similarity in blastp results
Popular Question 14 months ago, created a question with more than 1,000 views. For Format convert error while using Trinity Galaxy
Popular Question 21 months ago, created a question with more than 1,000 views. For Can I assemble a Eukaryote RNA-Seq using my laptop?
Popular Question 21 months ago, created a question with more than 1,000 views. For Format convert error while using Trinity Galaxy
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Format convert error while using Trinity Galaxy

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1254 users visited in the last hour