User: i19870503

gravatar for i19870503
i1987050310
Reputation:
10
Status:
New User
Location:
Australia
Last seen:
5 days, 17 hours ago
Joined:
5 years, 2 months ago
Email:
i********@gmail.com

Posts by i19870503

<prev • 13 results • page 1 of 2 • next >
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Comment: C: SnpEff annotation was not consistent with the original snp result
... ok, thanks both of you. ...
written 6 months ago by i1987050310
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SnpEff annotation was not consistent with the original snp result
... I use snpEff to annotate the snp result, but I found that the annotation of SNP wre not consistent with the SNP result. e.g.: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 AL123456.3 11820 . C G 9080.29 . AB=0;ABP=0;AC=2;AF=1; ...
snp written 7 months ago by i1987050310
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Comment: C: cuffdiff was killed without any information?
... You are right, it runs without any error whtn I try to use less samples run the command. So do you have any idea to limit the memory usage of cuffdiff?   ...
written 4.4 years ago by i1987050310
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cuffdiff was killed without any information?
... I have 29 samples to run cuffdiff, before cuffdiff it runs smoothly. But I run cuffdiff several hours it shows that : [17:23:59] Loading reference annotation and sequence. Warning: No conditions are replicated, switching to 'blind' dispersion method [17:24:41] Inspecting maps and determining fragm ...
rna-seq written 4.4 years ago by i1987050310 • updated 4.4 years ago by Daniel Swan13k
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Comment: C: how to modify sam file sort order
... One more question, if I convert the bam file to sam, could I modfiy the order munually. ...
written 4.4 years ago by i1987050310
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Comment: C: how to modify sam file sort order
... Ok, got it. Thanks very much. ...
written 4.4 years ago by i1987050310
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how to modify sam file sort order
... I got the error when I run cuffdiff Error: sort order of reads in BAMs must be the same so I use samtools view find that in this bam file, the others are sorted as chr1,chr2....not like this one. How to modify the order to make it as other file? @HD VN:1.0 SO:coordinate @SQ SN:chr10 ...
rna-seq written 4.4 years ago by i1987050310 • updated 4.4 years ago by Ashutosh Pandey11k
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Comment: C: Nothing in rfam_scan rusults.
... The test file comes from a smallRNAseq data, matching to miRNA is right. I want to know the distribution of all the reads wiht blast. ...
written 4.8 years ago by i1987050310
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Nothing in rfam_scan rusults.
... I use rfam_scan.pl to annotate the RNA-seq raw reads. But after run that there is nothing in the rusults file. the code: perl rfam_scan.pl_v_1.0.4 -o rfam.out.gff3 -blastdb Rfam.fasta Rfam.cm 1.fa -v read fasta file read CM library run blast pre-filter parse blast results run infernal search sear ...
rna-seq written 4.9 years ago by i1987050310
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Comment: C: How to anntate small-RNA seq reads distribution
... Thanks for reply, My species is pig, so the annotation is not very suffcient. I think blast is more acceptable method. ...
written 4.9 years ago by i1987050310

Latest awards to i19870503

Popular Question 4.1 years ago, created a question with more than 1,000 views. For cuffdiff was killed without any information?
Popular Question 4.1 years ago, created a question with more than 1,000 views. For how to modify sam file sort order
Popular Question 4.1 years ago, created a question with more than 1,000 views. For How to anntate small-RNA seq reads distribution
Popular Question 4.1 years ago, created a question with more than 1,000 views. For How could I use the Ensembl ncRNA fasta file to annotate my RNA-seq data

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