User: bioguy24

gravatar for bioguy24
bioguy24190
Reputation:
190
Status:
Trusted
Location:
Chicago
Last seen:
4 days, 12 hours ago
Joined:
4 years, 11 months ago
Email:
c******@luriechildrens.org

Posts by bioguy24

<prev • 217 results • page 1 of 22 • next >
0
votes
0
answers
38
views
0
answers
STAR-Fusion error while executing and produces some intermediates files
... I have run STAR and am now executing STAR-Fusion on the Chimeric.out.Junction.Out and it executes but I get the below error and no output is produced. I am not sure what the error means, am I missing something? Thank you :). **version** STAR-2.7.0f STAR-Fusion 1.6.0 **command** ST ...
star-fusion written 6 days ago by bioguy24190
0
votes
1
answer
91
views
1
answers
Comment: C: report every base in a bam using bed as input
... Thank you very much :). ...
written 5 weeks ago by bioguy24190
3
votes
1
answer
91
views
1
answer
report every base in a bam using bed as input
... Trying to output all lines (variant or reference) in the bed file using the below command. Most are SNP's but not all. The command does execute and produce the current output which is ok but why is it only 1 line from the bed? Is there a better approach? Using Samtools and Bcftools 1.9. Thank you :) ...
samtools bcftools written 5 weeks ago by bioguy24190 • updated 5 weeks ago by Pierre Lindenbaum120k
1
vote
3
answers
194
views
3
answers
Answer: A: compare two columns of two files
... Another awk: awk 'NR==FNR{c[$2]++;next};c[$1] > 0' file1 file2 ...
written 8 weeks ago by bioguy24190
0
votes
0
answers
131
views
0
answers
Comment: C: correct mark duplicated error using python and pysam to filter out secondary ali
... I have re-mapped and markduplicates seems ok but I am curious if the python script is close? Thank you :). ...
written 8 weeks ago by bioguy24190
0
votes
3
answers
1.1k
views
3
answers
Answer: A: Extract gene names from annotated vcf file
... I have not used SNPeff, but if the gene name is always in the fourth field seperated by | awk -F'|' '{print $4}' ...
written 8 weeks ago by bioguy24190
0
votes
0
answers
131
views
0
answers
correct mark duplicated error using python and pysam to filter out secondary alignments
... I am new to python and trying to learn. The below is an attempt to filter out secondary reads in a all bam files in a directory using pysam. I ran mark duplicates and got an error on several bam files due to secondary alignments. I added comments to each line to illustrate my thought process. I thin ...
python pysam written 8 weeks ago by bioguy24190
3
votes
2
answers
421
views
6 follow
2
answers
samtools covert to bam, sort and index all gz.sam
... The below bash script utilizes samtools in parellel to convert all gz.sam in a directory, sort, and index (I think). However, it seems to be processing a long time and I am not sure if it is indexed. Is there a better, more-efficient way? Without the .gz it is much faster. I am using samtools 1.9. T ...
parellel samtools written 5 months ago by bioguy24190 • updated 5 months ago by cmdcolin1.2k
0
votes
1
answer
552
views
1
answers
Comment: C: gatk vqsr --recal-file error
... Thank you very much :). ...
written 10 months ago by bioguy24190
2
votes
1
answer
552
views
1
answer
gatk vqsr --recal-file error
... In GATK 4.0.6.0 I am getting the below error using the command: gatk VariantRecalibrator \ -R /home/cmccabe/Desktop/fastq/resources/ucsc.hg19.fasta \ -V NA12878.vcf.gz \ --resource hapmap,known=false,training=true,truth=true,prior=15.0:/home/cmccabe/Desktop/f ...
gatk vqsr written 10 months ago by bioguy24190 • updated 10 months ago by Santosh Anand4.8k

Latest awards to bioguy24

Popular Question 5 months ago, created a question with more than 1,000 views. For query using mysql on ucsc table browser
Popular Question 5 months ago, created a question with more than 1,000 views. For bash loop to count variants using vcftools
Popular Question 10 months ago, created a question with more than 1,000 views. For query using mysql on ucsc table browser
Popular Question 10 months ago, created a question with more than 1,000 views. For bash loop to count variants using vcftools
Popular Question 10 months ago, created a question with more than 1,000 views. For coverageBed with -g option ?
Popular Question 10 months ago, created a question with more than 1,000 views. For run picard on all bam files in directory
Popular Question 10 months ago, created a question with more than 1,000 views. For fastq or bam file for additional alignment
Popular Question 10 months ago, created a question with more than 1,000 views. For correct way to add path to ubuntu 14.04.3
Popular Question 10 months ago, created a question with more than 1,000 views. For aligned or unaligned bam file
Popular Question 10 months ago, created a question with more than 1,000 views. For vcftools tools install on ubuntu 14.04
Popular Question 10 months ago, created a question with more than 1,000 views. For Need recommendation for a virtual machine or linux cluster for ngs analysis
Great Question 11 months ago, created a question with more than 5,000 views. For convert gene name to entrez id
Popular Question 14 months ago, created a question with more than 1,000 views. For Need recommendation for a virtual machine or linux cluster for ngs analysis
Popular Question 14 months ago, created a question with more than 1,000 views. For coverageBed with -g option ?
Popular Question 14 months ago, created a question with more than 1,000 views. For run picard on all bam files in directory
Popular Question 14 months ago, created a question with more than 1,000 views. For fastq or bam file for additional alignment
Popular Question 14 months ago, created a question with more than 1,000 views. For aligned or unaligned bam file
Popular Question 14 months ago, created a question with more than 1,000 views. For vcftools tools install on ubuntu 14.04
Popular Question 14 months ago, created a question with more than 1,000 views. For bowtie2 install on ubuntu
Popular Question 16 months ago, created a question with more than 1,000 views. For Need recommendation for a virtual machine or linux cluster for ngs analysis
Popular Question 16 months ago, created a question with more than 1,000 views. For coverageBed with -g option ?
Popular Question 18 months ago, created a question with more than 1,000 views. For Need recommendation for a virtual machine or linux cluster for ngs analysis
Popular Question 18 months ago, created a question with more than 1,000 views. For aligned or unaligned bam file
Popular Question 20 months ago, created a question with more than 1,000 views. For aligned or unaligned bam file
Popular Question 20 months ago, created a question with more than 1,000 views. For ion torrent alignment software

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 957 users visited in the last hour