User: Jackie

gravatar for Jackie
Jackie30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
2 weeks ago
Joined:
4 years, 8 months ago
Email:
d*******@gmail.com

about me

Posts by Jackie

<prev • 23 results • page 1 of 3 • next >
0
votes
1
answer
111
views
1
answer
How to output a pdf with both tables and plots using perl
... Hi, I am using perl PDF:Table module to generate a pdf file. In the PDF, there will be 4 sections, 1st, 2nd, and 4th sections are all tables, and the 3rd section needs to be a histogram. Can someone advise how can this be done? I know how to make a PDF with all the sections being tables, but not ...
perl histogram pdf:table plot written 14 days ago by Jackie30 • updated 14 days ago by shenwei3561.6k
0
votes
0
answers
109
views
0
answers
How to map NCBI contig positions to chromosome positions
... I need to make a file which includes all coordinates for human 37.13 (NCBI) ribosomal RNAs. I have downloaded the NCBI 'ref_GRCh37.p13_scaffolds.gff3.gz' file from this link ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ This gff3 file does include the coordinat ...
ncbi contig ribosomal grch37.13 written 19 days ago by Jackie30 • updated 19 days ago by genomax222k
2
votes
1
answer
130
views
1
answer
Use Bowtie to trim reads in fastq files
... I usually use Bowtie as an aligner, but I wonder whether I can use Bowtie as a trimmer as well? I tried the below command line: bowtie -1 read1.fastq -2 read2.fastq --trim5 2 --un unaligned --al aligned > aligned.bam I wanted bowtie to trim the first 2bps at the 5prime end, and outpu ...
trim bowite written 20 days ago by Jackie30 • updated 20 days ago by Brian Bushnell9.7k
1
vote
0
answers
142
views
0
answers
Difference between the two models in manta
... What is the difference between the manta disease model (--tumorBam) and germline model (--bam)? i.e, different calling algorithms, different filtering criteria? Is there some detailed documentation on that? Thanks ...
manta rna-seq written 5 weeks ago by Jackie30
1
vote
0
answers
144
views
0
answers
Questions about the splitting/spannings reads reported by manta
... Has anyone used the SV caller manta? I have a couple of questions regarding the splitting/spanning reads reported by manta: 1) In the manta output 'diploidSV.vcf', there are PR and SR tags, which mean 'Spanning paired-read support for the ref and alt alleles in the order listed' and 'Split reads fo ...
manta splitting reads spanning reads rna-seq written 5 weeks ago by Jackie30 • updated 22 days ago by Biostar ♦♦ 10
1
vote
1
answer
147
views
1
answer
How to align reads using bowtie against multiple customized reference files
... Hi, I am trying to use Bowtie to align RNA-seq fastq files to a set of small reference fasta files (i.e., ribosomal reference, mitochondrial reference, all for human). I've learned some groups have done that, but technically, I don't know how to implement that. As far as I know, Bowtie does not d ...
bowtie written 5 weeks ago by Jackie30
0
votes
1
answer
170
views
1
answers
Comment: C: Alignment stats summary by STAR aligner, please help!
... Thanks apa@stowers for the very detailed response, that helps. Yes, I found the spliced alignment particularly confusing. And, I also tried samtools flagstat for stats on read1/read2 separately, seems it would not give you the number same as in STAR log output. I.e., the total number of reads in ea ...
written 5 weeks ago by Jackie30
4
votes
1
answer
170
views
1
answer
Alignment stats summary by STAR aligner, please help!
... Hi, I am using STAR to align RNA-seq data, and I would like to make a QC metrics report out of the STAR logs. I want to do something like below: Total Aligned Reads for read1 and read 2 (% Reads) Abundant Reads for read1 and read 2 (% Reads) Unaligned Reads for read1 and read 2 (% Reads) Reads ...
alignment qc star rna-seq written 5 weeks ago by Jackie30
0
votes
1
answer
149
views
1
answers
Answer: A: Tophat-fusion-post running errors
... Hi, Can anyone share some experience or provide some insights to this issue? Thanks! ...
written 11 weeks ago by Jackie30
0
votes
1
answer
149
views
1
answer
Tophat-fusion-post running errors
... Hi, I am running tophat-fusion-post using this command line: ./tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 / The tophat-fusion output folder is in the same directory where I am running the command line. and I got below error messages: Traceback (most re ...
tophat-fusion-post bowtie python error written 11 weeks ago by Jackie30

Latest awards to Jackie

Popular Question 4 weeks ago, created a question with more than 1,000 views. For tophat-fusion for gene fusion detection

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1075 users visited in the last hour