User: wangyang703092

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Posts by wangyang703092

<prev • 24 results • page 1 of 3 • next >
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Problem in the results of StringTie
... Hi, When I quantifies expression levels for the features of the transcriptome using StringTie, some results in the output really made me confused. In the `e_data.ctab`,the coverage of a transcripts is really high and actually many reads mapped to the reference genome at this site. e_id chr ...
stringtie rna-seq written 3.7 years ago by wangyang70309290 • updated 2.9 years ago by jonasmst290
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How can I calculate selective pressure with opal mutations?
... Hi guys, I have a list of protein coding DNA sequences to calculate dN/dS but some of these have mutations which introduce a premature stop codon. So, how to calculate the ratio, just use the sequence before the stop codon or just delete the stop codon? And, is this mutation a mark of strong positiv ...
selective pressure evolution dnds written 4.3 years ago by wangyang70309290
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Comment: C: Problem about Samtools Mpileup
... Thank you so much for your help 在2015年01月06日 17:50,Devon Ryan on Biostar 写道: Activity on a post you are following on Biostar User Devon Ryan wrote Comment: Problem about Samtools Mpileup: bcftools call -c would seem correct. You may reply via email or visit C: Problem about Samtools Mpileup ...
written 4.9 years ago by wangyang70309290
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Comment: C: Problem about Samtools Mpileup
... Do you know how to set the bcftools call options because i'm not familiar to it. I used bcftools view -cg before, and now i use bcftools call -c ,do you think it's correct? ...
written 4.9 years ago by wangyang70309290
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Comment: C: Problem about Samtools Mpileup
... I did what you told me, my command is samtools mpileup --ff 1540 -f aaa.fasta aln.bam, but it has no difference with the result without --ff option. So i download the lastest version samtools-1.1 and bcftools-1.1, when using -ff 1540 or string[UNMAP,QCFAIL,DUP], it does work! Firstly, i used bcftool ...
written 4.9 years ago by wangyang70309290 • updated 4.9 years ago by Devon Ryan92k
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Comment: C: Problem about Samtools Mpileup
... Hi,i found that --ff is a filter option,but it can only accept INT ,i don't know how to set that,do you have any idea? ...
written 4.9 years ago by wangyang70309290
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Comment: C: Problem about Samtools Mpileup
... Thanks for your patience,I would like to use the secondary alignments to call SNP, how can I set the mpileup options.When I read the manual, I haven't find the --f option 在2015年01月06日 00:47,Devon Ryan on Biostar 写道: Activity on a post you are following on Biostar User Devon Ryan wrote Comment: Probl ...
written 4.9 years ago by wangyang70309290
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Comment: C: Problem about Samtools Mpileup
... Sorry Devon, what's secondary alignments, and where is the --ff option(in bowtie2?) 在2015年01月06日 00:18,Devon Ryan on Biostar 写道: Activity on a post you are following on Biostar User Devon Ryan wrote Comment: Problem about Samtools Mpileup: All but one of those are secondary alignments. Given that t ...
written 4.9 years ago by wangyang70309290
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Comment: C: Problem about Samtools Mpileup
... Thanks,but why you said the alignments will always be ignored,aren't the reads mapped to the region between 42449 and 42469? I am new to mpileup. 在2015年01月05日 23:58,Devon Ryan on Biostar 写道: Activity on a post you are following on Biostar User Devon Ryan wrote Comment: Problem about Samtools Mpileup ...
written 4.9 years ago by wangyang70309290
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Problem about Samtools Mpileup
... I have been generating consensus sequences from a Bowtie2-aligned BAM file using the following script: samtools mpileup -d 100000 -Q 0 -q 0 -f Reference.fasta input.bam in the pileup file, the consensus sequence has a gap where I can clearly see reads that map to the reference, in the pileup fi ...
assembly samtools snp written 4.9 years ago by wangyang70309290 • updated 4.4 years ago by Biostar ♦♦ 20

Latest awards to wangyang703092

Popular Question 4.1 years ago, created a question with more than 1,000 views. For memory requirments of velvet tool (de novo assembly)
Popular Question 4.8 years ago, created a question with more than 1,000 views. For RNA-seq read count data normalizaiton using housekeeping genes

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