User: ddzhangzz

gravatar for ddzhangzz
ddzhangzz40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
11 hours ago
Joined:
3 years, 8 months ago
Email:
d********@gmail.com

Posts by ddzhangzz

<prev • 41 results • page 1 of 5 • next >
0
votes
0
answers
91
views
0
answers
How has StringTie caculated the transcript coverage?
... Recently I have used Stringtie to compute the reads of RNASeq mapping to transcripts. There are two transcripts of a gene with exactly same length and number of exons (as well as the assembly structure of the two transcripts) and I found the coverages were very different from each other. ##tra ...
rna-seq written 11 days ago by ddzhangzz40
2
votes
1
answer
213
views
1
answer
How to download NCBI sequences using a list of Refseq IDs?
... I have a list of Refseq IDs such as: [1] "NM_010220" "NM_001290393" "NM_007743" "NM_175344" "NM_029432" [6] "NM_001111121" "NM_153399" "NM_007592" "NM_181402" "NM_013737" 11] "NM_007737" "NM_029967" "NM_146062" "NM_019477" "NM_172746" 16] "NM_0241 ...
R written 10 weeks ago by ddzhangzz40
2
votes
1
answer
192
views
1
answer
How to screen TCGA population for a specific mutation using a COSMIC ID
... I am working on a TCGA breast cancer dataset and wanted to check the prevalence of a specific mutation in this population. If I found an interested mutation from COSMIC, I am wondering how I can link or screen this COSMIC ID (e.g. COSM43759) in the TCGA population. Does somebody have experiences on ...
next-gen written 12 weeks ago by ddzhangzz40 • updated 11 weeks ago by Kevin Blighe11k
0
votes
1
answer
238
views
1
answers
Comment: C: Why Trimmoatic assign paired sequences to unpaired after adapter trimming
... Thanks for your reply @Brian Bushnell. My sequence length is 151bp and I guess the length may be unlikely below 50bp even after adapter timmimg off. In what reasons do you think the sequence was eliminated? ...
written 3 months ago by ddzhangzz40
0
votes
1
answer
238
views
1
answer
Why Trimmoatic assign paired sequences to unpaired after adapter trimming
... I manually checked the output of the Trimmomatic and was confused that a paired seqs were assigned to unpaired in the output. Here is my Trimmomatic command line: java -Xms8g -jar Trimmomatic.jar PE -threads 6 -phred33 sample1_R1.fastq.gz sample1_R2.fastq.gz sample1_forward_paired.fastq.gz samp ...
rna-seq written 3 months ago by ddzhangzz40
0
votes
0
answers
241
views
0
answers
Trimmomatic: Missing sequence line from record
... My RNASeq data appear about 3% adapter contamination and I was trying to trim them using Trimmomatic (v.0.36) but it seems it doesn't work correctly. I got below message a second after I run the program: TrimmomaticPE: Started with arguments: ...
rna-seq written 4 months ago by ddzhangzz40
0
votes
1
answer
321
views
1
answers
Comment: C: How to subset a UCSC table
... Thanks! It works. Never thought it was caused by name...:(. ...
written 7 months ago by ddzhangzz40
0
votes
1
answer
321
views
1
answers
Comment: C: How to subset a UCSC table
... $ ll /data/projects/JingChen-TCGA/Alternative_splicing/Data/UCSC/local total 8 -rw-r--r-- 1 3849 Jun 8 14:20 TP53-ensGene.txt -rw-r--r-- 1 4015 Jun 8 11:21 TP53-Homo_sapiens_Transcript_Summary.txt ...
written 7 months ago by ddzhangzz40
2
votes
1
answer
321
views
1
answer
How to subset a UCSC table
... I downloaded `ensGene.txt` file from [UCSC here][1] and wanted to create custom GFF annotation for [MISO][2]. I can generate the GFF annotation using the entire ensGene.txt file but I am only interested to generate for a small subset. Then I create a subset by grep such like: $grep ENSG00000141 ...
assembly written 7 months ago by ddzhangzz40
0
votes
1
answer
222
views
1
answers
Comment: C: Check the DNA strands source information of paired RNA-Seq fastq data
... Thanks @Devon Ryan! Could you have some explanation of the -f and -F options? And I got same numbers from my case: samtools view -c -f 32 -F 256 C92LDANXX_s8_1_B01_0249_SL152940Aligned.out.bam 19770944 samtools view -c -f 16 -F 256 C92LDANXX_s8_1_B01_0249_SL152940Aligned.out.bam 1 ...
written 8 months ago by ddzhangzz40

Latest awards to ddzhangzz

Popular Question 7 months ago, created a question with more than 1,000 views. For Calculate the fold change between two groups
Popular Question 8 months ago, created a question with more than 1,000 views. For Calculate the fold change between two groups
Popular Question 13 months ago, created a question with more than 1,000 views. For plink analysis including covariates and gxe
Scholar 21 months ago, created an answer that has been accepted. For A: Align RNASeq reads to combined genomes

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 459 users visited in the last hour