User: Santosh Anand

gravatar for Santosh Anand
Santosh Anand2.2k
Reputation:
2,250
Status:
Trusted
Location:
Last seen:
6 hours ago
Joined:
1 year, 2 months ago
Email:
s************@gmail.com

Posts by Santosh Anand

<prev • 388 results • page 1 of 39 • next >
0
votes
1
answer
130
views
1
answers
Comment: C: fastqc: kmer-content failed
... Did you check the other read pair why it not mapping? May be this is adaptor contamination, may be low quality. And one of your problems is the `--very-sensitive-local` mode, which will bias bowtie2 to look for local instead of end-to-end match. Try running with default params. ...
written 18 hours ago by Santosh Anand2.2k
0
votes
0
answers
62
views
0
answers
Comment: C: get variables in two separate lines
... And what's the problem with option A? why you need to keep all the data of a file inside a variable ?! PS: And I'll tell you, don't play with the white-space characters inside a variable; you are definitely going to burn and it hurts. PPS: This is happening because the bash shell splits the words ...
written 4 days ago by Santosh Anand2.2k
1
vote
3
answers
101
views
3
answers
Answer: A: get build 37 positions from dbSNP rsIDs
... One of the easiest ways is to use dbSNP database pre-formatted in annovar format from here (v147) http://www.openbioinformatics.org/annovar/download/hg19_avsnp147.txt.gz It looks like this: 1 10019 10020 TA T rs775809821 1 10020 10020 A - rs775809 ...
written 6 days ago by Santosh Anand2.2k
2
votes
0
answers
152
views
0
answers
Comment: C: BWA: Why paired reads mapped to different chromosome?
... You might have fusion genes, like [Philadelphia Chromosome][1]. Normally, an aligner will align wherever it finds the best match. The best match will be decided by some sort of final score, the calculation of which could be tuned according to the experimental need by changing the parameters of alig ...
written 6 days ago by Santosh Anand2.2k
0
votes
0
answers
163
views
0
answers
Comment: C: EOF marker is absent
... Can you paste the verbatim error message here? ...
written 6 days ago by Santosh Anand2.2k
0
votes
0
answers
105
views
0
answers
Comment: C: picard MarkDuplicates find EOF problem
... **EOF may or may not be present**, *but it was not expected in either case* (means that the bam file was end prematurely, owing to some corruption) ...
written 7 days ago by Santosh Anand2.2k
0
votes
0
answers
105
views
0
answers
Comment: C: picard MarkDuplicates find EOF problem
... There is a difference between EOF not present and premature EOF - in the later case, the EOF was probably present, but it was not expected. It means that the bam may be corrupted. You may try converting bam -> sam and then sam back to bam, if it resolves the problem. ...
written 7 days ago by Santosh Anand2.2k
1
vote
1
answer
140
views
1
answers
Comment: C: Extract Bibliographic Reference from GEO dataset using EFetch?
... This whole episode has become a detective movie for me! The main Q I am trying to get answer is that if I am able to do it at my end, why you are not? If the format is not supported by API for you, it must be the same for me. Also XML is standard format for data exchange; don't know why you have to ...
written 7 days ago by Santosh Anand2.2k
0
votes
1
answer
130
views
1
answers
Comment: C: fastqc: kmer-content failed
... Happy that it is resolved. I've moved my comment to answer. ...
written 7 days ago by Santosh Anand2.2k
3
votes
1
answer
130
views
1
answers
Answer: C: fastqc: kmer-content failed
... I would not be too much worried about the k-mer content unless there are other warning flags in QC. Moreover, the 5'-end has some bias for priming https://sequencing.qcfail.com/articles/positional-sequence-bias-in-random-primed-libraries/ What is your library (RNA-seq)? ...
written 7 days ago by Santosh Anand2.2k

Latest awards to Santosh Anand

Scholar 7 days ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 7 days ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 9 days ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 11 days ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Commentator 11 days ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Commentator 12 days ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Teacher 12 days ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Appreciated 12 days ago, created a post with more than 5 votes. For A: read.table does not read in all rows!
Scholar 12 days ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 13 days ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 13 days ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 13 days ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 13 days ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 20 days ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 26 days ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 26 days ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 4 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 5 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 5 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 5 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 5 weeks ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 665 users visited in the last hour