User: Satyajeet Khare

gravatar for Satyajeet Khare
Satyajeet Khare1.1k
Reputation:
1,110
Status:
Trusted
Location:
Pune, India
Scholar ID:
Google Scholar Page
Last seen:
12 hours ago
Joined:
1 year, 8 months ago
Email:
s*************@gmail.com

Posts by Satyajeet Khare

<prev • 249 results • page 1 of 25 • next >
0
votes
0
answers
150
views
0
answers
Comment: C: Major challenges of aligning the NGS data
... Understanding the scientific question. ...
written 18 days ago by Satyajeet Khare1.1k
0
votes
1
answer
130
views
1
answers
Comment: C: DGE on protein-coding and lncRNAs separately?
... Can you provide more details? You need to generate countmatrix of entire gene set and perform DGE analysis on that. You can shortlist genes of your interest (protein coding/non-coding) afterwards. ...
written 18 days ago by Satyajeet Khare1.1k
1
vote
1
answer
160
views
1
answers
Comment: C: How many cell lines for RNA-seq comparisons?
... Minimum two biological replicates each are generally recommended. ~30 - 40 million reads per sample are sufficient in my experience. ...
written 22 days ago by Satyajeet Khare1.1k
1
vote
0
answers
182
views
0
answers
Comment: C: Cutoff for TPM value
... Repeat of [this][1] question? [1]: https://www.biostars.org/p/238309/ ...
written 5 weeks ago by Satyajeet Khare1.1k
0
votes
0
answers
161
views
0
answers
Comment: C: Question about mapping motif binding sites to genome location
... Did you try using BLAT? P.S. Actually, did you try Ctrl+F in some sequence editor? Sequence editors (e.g. APE) search sequence on either strand. Once you know the pattern, it will be easy in future. ...
written 5 weeks ago by Satyajeet Khare1.1k
0
votes
2
answers
235
views
2
answers
Comment: C: How to run a Perl script
... The script is a part of [ea-utils][1] package. Just check the readme and [build instructions][2]. [1]: https://github.com/ExpressionAnalysis/ea-utils [2]: https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/Compiling.md ...
written 6 weeks ago by Satyajeet Khare1.1k
1
vote
1
answer
206
views
1
answers
Comment: C: Differential gene expression based on "exon" or "CDS"?
... Exons. Differential expression analysis utilizes gene annotation file which contains full length transcripts, including 5' and 3' UTRs. ...
written 6 weeks ago by Satyajeet Khare1.1k
0
votes
2
answers
388
views
2
answers
Comment: C: bash script for RNA seq analysis
... You may have to create output folders beforehand. Also, assuming forward and reverse read files end with R1 and R2 and not 1 and 2, I changed the end of the command. for i in $(ls *.fastq | rev | cut -c 9- | rev | uniq); do tophat2 -o ${i}tout -G /run/media/punit/data2/gencode.v21.ann ...
written 6 weeks ago by Satyajeet Khare1.1k
0
votes
0
answers
765
views
0
answers
Comment: C: hisat2-build failed with 'is not reverse-deterministic, so reverse-determinize'2
... Please move your comment to comment section (add comment) as it does not answer the question. ...
written 6 weeks ago by Satyajeet Khare1.1k
0
votes
0
answers
765
views
0
answers
Comment: C: hisat2-build failed with 'is not reverse-deterministic, so reverse-determinize'2
... Can you type your entire build command? Memory usage is expected. You can check the manual. ...
written 6 weeks ago by Satyajeet Khare1.1k

Latest awards to Satyajeet Khare

Scholar 7 weeks ago, created an answer that has been accepted. For A: error in tophat2
Guru 9 weeks ago, received more than 100 upvotes.
Scholar 9 weeks ago, created an answer that has been accepted. For A: error in tophat2
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
Scholar 9 weeks ago, created an answer that has been accepted. For A: error in tophat2
Scholar 10 weeks ago, created an answer that has been accepted. For A: error in tophat2
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
Scholar 3 months ago, created an answer that has been accepted. For A: error in tophat2
Scholar 3 months ago, created an answer that has been accepted. For A: error in tophat2
Popular Question 4 months ago, created a question with more than 1,000 views. For fastq dump error
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
Scholar 11 months ago, created an answer that has been accepted. For A: error in tophat2
Scholar 12 months ago, created an answer that has been accepted. For A: error in tophat2
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
Scholar 13 months ago, created an answer that has been accepted. For A: error in tophat2
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
Centurion 13 months ago, created 100 posts.
Scholar 14 months ago, created an answer that has been accepted. For A: error in tophat2
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
Supporter 14 months ago, voted at least 25 times.
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be
Scholar 14 months ago, created an answer that has been accepted. For A: error in tophat2
Appreciated 14 months ago, created a post with more than 5 votes. For A: Differentiall analysis of chip-deq data
Scholar 14 months ago, created an answer that has been accepted. For A: error in tophat2
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: I am really pissed off by the bioinformatics software world. Do/can we have a be

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 696 users visited in the last hour