User: Jackie

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Jackie40
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40
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New User
Location:
United States
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4 days, 17 hours ago
Joined:
4 years, 10 months ago
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Posts by Jackie

<prev • 26 results • page 1 of 3 • next >
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Comment: A: GT tag in VCF spec
... Thank you very much. This is helpful! ...
written 12 days ago by Jackie40
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GT tag in VCF spec
... Hi, Is GT tag in the FORMAT col a required tag by VCF spec? If a VCF does not have GT tag, is it still a valid VCF? Or put it another way, what is the minimum information that makes a VCF valid? Thanks ...
vcf gt tags valid written 12 days ago by Jackie40
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What does 'frac' mean in cufflinks output transcripts.gtf
... In Cufflinks output transcripts.gtf, there is a field called 'frac'. What does that mean? chr1 Cufflinks transcript 18957500 19062632 361 + . gene_id "PAX7"; transcript_id "NM_002584.2"; FPKM "218.4530519923"; frac "0.219171"; conf_lo "200.428676"; conf_h ...
fpkm cufflinkts frac written 4 weeks ago by Jackie40
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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 7 weeks ago by Jackie40 • updated 7 weeks ago by shenwei3562.3k
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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 7 weeks ago by Jackie40 • updated 7 weeks ago by genomax224k
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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 7 weeks ago by Jackie40 • updated 7 weeks ago by Brian Bushnell10k
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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 10 weeks ago by Jackie40 • updated 6 days ago by Chris Saunders100
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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 10 weeks ago by Jackie40 • updated 6 days ago by Chris Saunders100
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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 10 weeks ago by Jackie40
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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 10 weeks ago by Jackie40

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Popular Question 9 weeks ago, created a question with more than 1,000 views. For tophat-fusion for gene fusion detection

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