User: shl198

gravatar for shl198
shl198340
Reputation:
340
Status:
Trusted
Location:
United States
Last seen:
1 month, 4 weeks ago
Joined:
5 years, 1 month ago
Email:
s*************@yahoo.com

about me

Posts by shl198

<prev • 30 results • page 1 of 3 • next >
0
votes
1
answer
2.6k
views
1
answers
Comment: C: Augustus install mac
... Just thought it may be useful to others, I put my comment here. In my case, gcc version also matters. gcc4.8 works for bam2hints but not filterbam. I used gcc5.4 to compile filterbam successfully. ...
written 2.1 years ago by shl198340
4
votes
1
answer
1.2k
views
1
answer
Is checking clustering of technical replicates necessary for RNAseq?
... Dear all, I searched some threads, it seems like the standard recommendation for doing differential expression analysis is that: merge the fastq files of technical replicates together and then map to reference, count reads, do DE analysis. .  My question is that will it be safer if we map, count a ...
rna-seq technical replicates written 3.6 years ago by shl198340 • updated 3.6 years ago by Antonio R. Franco3.9k
5
votes
2
answers
1.3k
views
2
answers
relationship between coverage and expression level in RNAseq
... I wonder what is the relationship between the depth and gene expression level in RNAseq? For example, let's say I have RNAseq with 10M reads for one sample. If I use the same machine and generate 20M reads for the same sample, then except for the new detected genes, will the expression profile for ...
depth experiment design rna-seq expression written 3.7 years ago by shl198340 • updated 3.7 years ago by Gary450
0
votes
0
answers
1.8k
views
0
answers
Comment: C: How to get input for provean from vcf files annotated by snpeff?
... Thanks. Yes, there is coding variants, but provean also needs the whole protein sequence, After building the database using snpeff, there is only one .bin file, do you know how to get the whole protein sequence? The only way I can think of is using genome annotation file, but it would be a little bi ...
written 4.0 years ago by shl198340
2
votes
0
answers
1.8k
views
0
answers
How to get input for provean from vcf files annotated by snpeff?
... Hi all, I called variants using GATK, and annotated the results using snpeff. Since the organism is chinese hamster, there is not much information available. I want to use provean to predict the effects of variants. The problem is that the input for provean for non human/mouse model should be amino ...
vcf provean snpeff written 4.0 years ago by shl198340
0
votes
0
answers
1.2k
views
0
answers
detect SNPs using DNAseq fastq files which were used to assemble the genome
... Hello all, I find a problem that interest me. The chinese hamster genome was assembled using DNAseq. And when I tried to use the same DNAseq to call SNPs, it detected some SNPs. My question is: the assembly should not change the sequence, so there should be no SNPs if I use the same DNAseq which wa ...
assembly dna-seq snp written 4.2 years ago by shl198340
0
votes
1
answer
4.1k
views
1
answers
Comment: C: Why is pre formatted refseq database larger than nt database in blastdb?
... Hi, I just wonder how you get the information of Molecule Type:mixed DNA Update date:2014/07/24 Number of sequences:23840180. And also the number of bases? Thanks. ...
written 4.4 years ago by shl198340
0
votes
1
answer
1.9k
views
1
answers
Comment: C: Bowtie2 treats reads as not mapping even if the reads have exact same sequences
... Thank you very much. I will try STAR.  ...
written 4.4 years ago by shl198340
0
votes
1
answer
1.9k
views
1
answers
Comment: C: Bowtie2 treats reads as not mapping even if the reads have exact same sequences
... Hi Devon, thank you very much. I just tried mapping using bowtie2 directly instead of tophat, the result increased a little, and I also blast the unmapped reads, most of them mapped to mouse ribosomal RNA. I didn't change the annotation file, and I made sure there are rRNA reference in the gff file ...
written 4.4 years ago by shl198340
5
votes
1
answer
1.9k
views
1
answer
Bowtie2 treats reads as not mapping even if the reads have exact same sequences with reference?
... Hi all, I aligned my RNA-seq against reference genome using tophat, I used the default aligner bowtie2.  And also the default parameters:  tophat -p 8 -G $annotation -o out $database L1_1.fq.gz L1_2.fq.gz After got the results, I found out that in the unmapped.bam file, some reads have exact sam ...
bowtie2 quality tophat rna-seq written 4.4 years ago by shl198340 • updated 4.4 years ago by Devon Ryan86k

Latest awards to shl198

Popular Question 9 months ago, created a question with more than 1,000 views. For Is checking clustering of technical replicates necessary for RNAseq?
Great Question 9 months ago, created a question with more than 5,000 views. For Bwa Mem Have Different Alignment Result When Using Different Threads
Popular Question 9 months ago, created a question with more than 1,000 views. For relationship between coverage and expression level in RNAseq
Popular Question 9 months ago, created a question with more than 1,000 views. For relationship between coverage and expression level in RNAseq
Popular Question 2.0 years ago, created a question with more than 1,000 views. For How to get input for provean from vcf files annotated by snpeff?
Student 2.0 years ago, asked a question with at least 3 up-votes. For Run Makeblastdb For Compressed File
Great Question 2.8 years ago, created a question with more than 5,000 views. For Bwa Mem Have Different Alignment Result When Using Different Threads
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Run Makeblastdb For Compressed File
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Can Igv View Blast+ Output File?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Can bowtie2-build index for gzipped file?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Run Makeblastdb For Compressed File
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Run Makeblastdb For Compressed File
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Bwa Mem Have Different Alignment Result When Using Different Threads
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Run Makeblastdb For Compressed File
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Why is pre formatted refseq database larger than nt database in blastdb?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Why is pre formatted refseq database larger than nt database in blastdb?
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Why is pre formatted refseq database larger than nt database in blastdb?
Good Answer 4.4 years ago, created an answer that was upvoted at least 5 times. For A: Bwa Mem Have Different Alignment Result When Using Different Threads
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Bwa Mem Have Different Alignment Result When Using Different Threads
Appreciated 4.9 years ago, created a post with more than 5 votes. For A: Bwa Mem Have Different Alignment Result When Using Different Threads
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Bwa Mem Have Different Alignment Result When Using Different Threads
Appreciated 4.9 years ago, created a post with more than 5 votes. For Bwa Mem Have Different Alignment Result When Using Different Threads
Good Question 4.9 years ago, asked a question that was upvoted at least 5 times. For Bwa Mem Have Different Alignment Result When Using Different Threads
Student 4.9 years ago, asked a question with at least 3 up-votes. For Bwa Mem Have Different Alignment Result When Using Different Threads

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1812 users visited in the last hour