User: prasundutta87

gravatar for prasundutta87
prasundutta87280
Reputation:
280
Status:
Trusted
Location:
Last seen:
8 hours ago
Joined:
1 year, 10 months ago
Email:
p************@gmail.com

Posts by prasundutta87

<prev • 140 results • page 1 of 14 • next >
2
votes
1
answer
146
views
1
answers
Answer: A: Paired-end flag for singleton
... I believe when a read is singleton, it is 'unpaired' for a paired-end sequencing read. So, you can check for reads whose flags are not set to 1 which is the flag for 'paired-end' reads.. ...
written 25 days ago by prasundutta87280
0
votes
0
answers
150
views
0
answers
Comment: C: manhattan plot with Fst values
... Right..you need to import your input data in R first before you do anything with it... ...
written 26 days ago by prasundutta87280
0
votes
0
answers
150
views
0
answers
Comment: A: manhattan plot with Fst values
... Please post your whole code here. How have you imported the data in R? ...
written 26 days ago by prasundutta87280
0
votes
2
answers
149
views
2
answers
Comment: C: no gene_id for tRNA in GFF3
... I could only moderate my post to make it as an 'answer'..the main answer should be your first reply.. ...
written 7 weeks ago by prasundutta87280
1
vote
2
answers
149
views
2
answers
Comment: C: no gene_id for tRNA in GFF3
... Thanks a lot Lieven! This was very helpful. ...
written 7 weeks ago by prasundutta87280
0
votes
2
answers
149
views
2
answers
Comment: C: no gene_id for tRNA in GFF3
... I was also thinking of an option to give dummy gene and transcript IDs to them.. but haven't done that yet..can that be a workaround as well? ...
written 7 weeks ago by prasundutta87280
0
votes
2
answers
149
views
2
answers
Answer: C: no gene_id for tRNA in GFF3
... Hmm..ok..so its better to just drop them off in our case. ...
written 7 weeks ago by prasundutta87280
3
votes
2
answers
149
views
2
answers
no gene_id for tRNA in GFF3
... Hi, In one of the non-human organisms, GFF3 annotation file downloaded from NCBI genome FTP, there were some tRNA annotations (tRNA-Glu, tRNA-Ser, etc) in the mitochondrial genome that did not have a gene_id. They don't have any transcript features associated with them as well. Is it a usual annota ...
gff3 annotation gtf written 7 weeks ago by prasundutta87280
0
votes
1
answer
226
views
1
answers
Answer: A: Is HISAT2 able to output only the best alignment?
... When you say 'best alignment', I believe you mean 'primary alignment'. According to the HISAT2 manual (https://ccb.jhu.edu/software/hisat2/manual.shtml), 'Primary alignments mean alignments whose alignment score is equal or higher than any other alignments. It is possible that multiple distinct alig ...
written 7 weeks ago by prasundutta87280
0
votes
0
answers
169
views
0
answers
Comment: C: allele specific expression (ASE) reference ratio plot query
... Hi Vitis, Thanks for the reply. I have not done that. My basic QC was limited to fastqc visualisation and trimming. I forgot to mention that the problematic samples are from total RNA-seq. My 14 samples have a mix of mRNA-seq and total RNA-seq samples. I have updated my post now. ...
written 8 weeks ago by prasundutta87280

Latest awards to prasundutta87

Popular Question 1 day ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Scholar 17 days ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Student 8 weeks ago, asked a question with at least 3 up-votes. For allele specific expression (ASE) reference ratio plot query
Popular Question 10 weeks ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Popular Question 12 weeks ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Popular Question 4 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Centurion 5 months ago, created 100 posts.
Supporter 7 months ago, voted at least 25 times.
Scholar 16 months ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: SNPEFF for de novo transcriptome annotation

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1083 users visited in the last hour