User: ag1194

gravatar for ag1194
ag11940
Reputation:
0
Status:
New User
Last seen:
5 months ago
Joined:
3 years, 2 months ago
Email:
a*****@gsbs.rutgers.edu

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by ag1194

<prev • 15 results • page 1 of 2 • next >
0
votes
3
answers
521
views
3
answers
Comment: C: Filtering sam/bam by using CIGAR deletion sites
... With samtools view & awk tools, I cannot keep the header in my output bam. Is there a way to have filtered bam with header with awk tool? Thanks!!! ...
written 7 months ago by ag11940
0
votes
3
answers
521
views
3
answers
Comment: A: Filtering sam/bam by using CIGAR deletion sites
... Thank you very much!!! I'll try and see samjdk first and also pysam to see the results. ...
written 7 months ago by ag11940
2
votes
3
answers
521
views
5 follow
3
answers
Filtering sam/bam by using CIGAR deletion sites
... Hi, I have a CLIP-Seq data and after mapping, I want to filter my sam files for reads containing deletion by using CIGAR & MAPQ >10. Is there a way in samtools to subset my sam file containing reads MAPQ>10 & with deletion? Thank you very much! ...
alignment next-gen written 7 months ago by ag11940 • updated 7 months ago by Geparada1.4k
0
votes
0
answers
632
views
0
answers
DEXSeq batch effects issue
... Hi I have a question about DEXSeq batch effect design. I followed the protocol from DEXSeq guideline to count in the batch effect. featureID <- as.factor(data $featureID) groupID <- as.factor(data $gene_symbol) design <- formula( ~ sample + exon + condition:exon ) formul ...
dexseq rna-seq written 2.2 years ago by ag11940
0
votes
1
answer
1.4k
views
1
answers
Comment: C: Calculating number of reads in a specific region from sam file
... great, let me check. Thanks! ...
written 2.9 years ago by ag11940
0
votes
1
answer
1.4k
views
1
answers
Comment: C: Calculating number of reads in a specific region from sam file
... I want to check the reads falls into specific region though. Not a defined exon. ...
written 2.9 years ago by ag11940
3
votes
1
answer
1.4k
views
1
answer
Calculating number of reads in a specific region from sam file
... Hi, Hi I have a mapped sequencing data in sam format (RNA). I want to calculate number of reads are on one region (let's say exon 10), then number of gene are on another region (lets say exon 11), then compare these two read number for each gene. So basically I have a table who contains two regio ...
rna-seq sequencing written 2.9 years ago by ag11940 • updated 2.9 years ago by geek_y9.8k
0
votes
0
answers
1.2k
views
0
answers
Comment: C: MISO: Warning: cannot parse their job IDs from the cluster submission system
... when I remove --use-cluster command, I immediately get the warning "WARNING - Thread batch-0 might have failed". ...
written 3.1 years ago by ag11940
0
votes
0
answers
1.2k
views
0
answers
Comment: C: MISO: Warning: cannot parse their job IDs from the cluster submission system
... I am very new at MISO. MISO manual says "MISO comes with basic functionality for running on a cluster" . While running MISO, command line says "executing: qsub" I suppose this is for cluster job scheduler. Other than that, I have no idea. ...
written 3.1 years ago by ag11940
0
votes
0
answers
1.2k
views
0
answers
MISO: Warning: cannot parse their job IDs from the cluster submission system
... Hi, I am running MISO and getting following warning: WARNING - Asked to wait on cluster jobs but cannot parse their job IDs from the cluster submission system. And in mysample.output/ directory, instead of having MISO run output, I have: batch-genes , batch--logs, cluster_scripts, logs, scripts_ ...
miso rna-seq written 3.1 years ago by ag11940

Latest awards to ag1194

Popular Question 2.0 years ago, created a question with more than 1,000 views. For MISO: Warning: cannot parse their job IDs from the cluster submission system
Popular Question 2.0 years ago, created a question with more than 1,000 views. For tophat2 0% mapping rate for strand-specific RNA-seq
Popular Question 2.0 years ago, created a question with more than 1,000 views. For tophat2 cannot find transcript file
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Calculating number of reads in a specific region from sam file

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