User: Prakash

gravatar for Prakash
Prakash1.2k
Reputation:
1,240
Status:
Trusted
Location:
India
Twitter:
gprakash047
Last seen:
8 hours ago
Joined:
3 years, 10 months ago
Email:
j********@gmail.com

Posts by Prakash

<prev • 110 results • page 1 of 11 • next >
1
vote
0
answers
84
views
0
answers
Comment: C: understanding bowtie2 unmapped reads
... There are two reason I could think of, either the reads are not mapping due to low quality reads or there is some contamination. I would try doing blast for few of the unmapped reads and see if I get some hits for contamination. ...
written 10 days ago by Prakash1.2k
2
votes
1
answer
106
views
1
answers
Comment: C: How to bin my count data for the entire genome?
... > bedtools coverage -a binned_genome.bed -b myfile.bed -sorted -g > mm10.txt This will give mean coverage across your binned genomic regions. you can also use genomeCoverage bed to get reads normalized per million. genomeCoverageBed -ibam -i -g mm10.fa -scale RPM ...
written 10 days ago by Prakash1.2k
1
vote
0
answers
84
views
0
answers
Comment: C: understadning bowtie2 unmapped reads
... If I just see your percent of aligned reads, I would say only one sample i.e IP_IgG1 has got some problem, rest appear to be fine, The problem could be due to efficiency of antibody, you might also look into total number of reads. How did you search for contamination ? ...
written 10 days ago by Prakash1.2k
0
votes
1
answer
109
views
1
answers
Comment: C: print non match to list lines of GTF file
... you are right SMK, there was actually empty line in the file Its working now. :) ...
written 10 days ago by Prakash1.2k
3
votes
1
answer
109
views
1
answers
Answer: C: print non match to list lines of GTF file
... Did above command worked, it didn't work for me, you can try using awk awk -F'"' 'NR==FNR{a[$1]++;next}!a[$2]' list_file GTF_file ...
written 11 days ago by Prakash1.2k
0
votes
2
answers
123
views
2
answers
Comment: C: convering mouse emsembl gene IDs to Gene names by bioMart and gconvert with no
... look at this [post][1] [1]: https://www.biostars.org/p/337072/#337073 ...
written 11 days ago by Prakash1.2k
4
votes
1
answer
106
views
1
answers
Answer: A: How to bin my count data for the entire genome?
... bedtools makewindows you might be looking for. you can divide your genome into bins of 10kb and then calculate coverage using your bam files. or may be you can use tag directory from homer as well. ...
written 12 days ago by Prakash1.2k
3
votes
1
answer
98
views
1
answers
Answer: C: Construct a gene co-expression network with WGCNA
... Try this link https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/ ...
written 21 days ago by Prakash1.2k
3
votes
3
answers
277
views
3
answers
Answer: A: Gene expression profile analysis
... There is another tool called [short-time series expression miner][1] [1]: http://www.cs.cmu.edu/~jernst/stem/ ...
written 6 weeks ago by Prakash1.2k
2
votes
1
answer
174
views
1
answers
Comment: C: How to assign the result of a command to a variable in shell script?
... Then you would have more delimiter in you string. I tried to to reproduce similar to your input and it worked. yes basename is great idea indeed. ...
written 6 weeks ago by Prakash1.2k

Latest awards to Prakash

Teacher 7 days ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Delete numbers in the tables column
Appreciated 14 days ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: How to add gene symbol to RNA-Seq data using R
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Guru 6 weeks ago, received more than 100 upvotes.
Centurion 7 weeks ago, created 100 posts.
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Popular Question 4 months ago, created a question with more than 1,000 views. For Finding instances of motifs near peaks
Appreciated 4 months ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Scholar 4 months ago, created an answer that has been accepted. For A: How to add colors to bar chart?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: How to add gene symbol to RNA-Seq data using R
Popular Question 7 months ago, created a question with more than 1,000 views. For Finding instances of motifs near peaks
Appreciated 7 months ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Gene Set Enrichment Analysis after DESeq2
Scholar 9 months ago, created an answer that has been accepted. For A: Gene Set Enrichment Analysis after DESeq2
Appreciated 9 months ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: How to add gene symbol to RNA-Seq data using R
Scholar 9 months ago, created an answer that has been accepted. For A: Gene Set Enrichment Analysis after DESeq2

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1790 users visited in the last hour