User: rizoic

gravatar for rizoic
rizoic230
Reputation:
230
Status:
Trusted
Location:
Last seen:
15 hours ago
Joined:
1 year, 7 months ago
Email:
r********@gmail.com

Posts by rizoic

<prev • 21 results • page 1 of 3 • next >
0
votes
0
answers
65
views
0
answers
Comment: C: Handling bwa double free or corruption related core dump on an HPC
... Thanks. Yes the program has been installed by the sys admin. I have tried the following option to tell the scheduler to allocate more memory explicitly. `bsub -n 6 -q -R "rusage[mem=8024]" 'bwa mem -t 6 t.fasta 1.fastq.gz 2.fastq.gz 2> log.txt|samtools sort -o test.bam'` However the core du ...
written 2 days ago by rizoic230
0
votes
0
answers
65
views
0
answers
Comment: C: Handling bwa double free or corruption related core dump on an HPC
... Thanks for your comment. I updated the post with details of the command line and operating system. The third suggestion actually makes sense. I did compile bwa newly from the source code but I think it still uses system libraries which may have an issue. Will try it with now with conda and see if ...
written 2 days ago by rizoic230
3
votes
0
answers
65
views
0
answers
Handling bwa double free or corruption related core dump on an HPC
... When I run bwa(v 0.7.17-r1188) through a scheduler on an HPC it randomly fails with a core dump and the log file mentions the error as `glibc: double free or corruption`. A google search on the error pointed to a env variable `MALLOC_CHECK_` whose value if changed can prevent this core dump. Accord ...
bwa snp written 2 days ago by rizoic230
0
votes
3
answers
172
views
3
answers
Answer: A: How to retrieve the SNP data from Bam file
... If you have your positions of interest in bed format you could look into [bam-readcount](https://github.com/genome/bam-readcount). You can run it simply as `bam-readcount -l regions.bed -f ref.fa file.bam` and get frequency values for all the nucleotides along with a bunch of additional info in c ...
written 4 months ago by rizoic230
2
votes
1
answer
316
views
1
answers
Comment: C: Has anyone here worked with CNCI before? EXHAUSTED
... Do you have `twoBitToFa` in your path. Taking a quick look at the source code [here](https://github.com/www-bioinfo-org/CNCI/blob/745e2d1942f0fa6c061f5308fdc876de430a114f/CNCI.py#L529) and the error it seems since `twoBitToFa` is not in the path the required fasta file creation failed. ...
written 5 months ago by rizoic230
0
votes
2
answers
292
views
2
answers
Comment: C: How to find those files name which contains specific symbol i.e. underscore sign
... The answer by @zx8754 is in R you will need to save it as a .R file and then execute it. ...
written 7 months ago by rizoic230
1
vote
2
answers
221
views
2
answers
Answer: C: .bash_profile shortcut to reverse a string
... You just need to remove the alias in your function and change the first argument to $1 as you are not interested in the length i.e. $#1 ``` revFunc() { echo ${1}|rev } ``` For reverse compliment you can change the function to be ``` revComp() { echo ${1}|tr "[ATGCatgc]" "[TACGtacg]"|r ...
written 8 months ago by rizoic230 • updated 8 months ago by RamRS26k
0
votes
1
answer
332
views
1
answers
Comment: C: Expression values for normal tissues
... Thanks. Z scores should give me a good idea about high/low expressed genes in the tumor. By chance are you aware of any resource to get an idea about the status of these genes in normal tissues? ...
written 9 months ago by rizoic230
4
votes
1
answer
332
views
1
answer
Expression values for normal tissues
... We have RNA seq `transcripts per million(TPM)` values for all genes in a tumor patient sample. However there was no sequencing done for normal samples from the same patient. We want to determine which genes are being over/under expressed in the tumor and having just its expression values is obviousl ...
rnaseq written 9 months ago by rizoic230 • updated 9 months ago by Kevin Blighe56k
1
vote
1
answer
1.4k
views
1
answers
Comment: C: How to remove singletons in a BAM file using samtools
... In your e.g. R1 is the singleton read since its mate is unmapped and thus R1 read will be removed when you filter for the flag `0x08`. ...
written 16 months ago by rizoic230

Latest awards to rizoic

Teacher 16 months ago, created an answer with at least 3 up-votes. For C: unable to load quant.sf files
Teacher 16 months ago, created an answer with at least 3 up-votes. For C: unable to load quant.sf files
Supporter 17 months ago, voted at least 25 times.
Scholar 17 months ago, created an answer that has been accepted. For C: unable to load quant.sf files
Teacher 17 months ago, created an answer with at least 3 up-votes. For C: unable to load quant.sf files
Scholar 17 months ago, created an answer that has been accepted. For C: unable to load quant.sf files
Teacher 17 months ago, created an answer with at least 3 up-votes. For C: unable to load quant.sf files

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1561 users visited in the last hour