User: apelin20

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apelin20470
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Canada
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1 year, 12 months ago
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3 years, 5 months ago
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Posts by apelin20

<prev • 128 results • page 1 of 13 • next >
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extract reads with given size range
... Hello, I did a smallRNA-Seq experiment where the sequencing provider was supposed to sequence small RNAs 15-25 nt. After trimming adapters, I see that there are reads ranging in size from 15 to 35 bp, but also reads that are 50 bp (the full length of the read). Since I sent total RNA, I assume the ...
fastq rna-seq smallrna-seq written 2.0 years ago by apelin20470 • updated 2.0 years ago by iraun3.3k
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Comment: C: N50 reduces after scaffolding
... It seems to have increased you genome size by 50 Mb, most of which are just NNNN sequences. Because the genome size is now larger, N50 changes. Are you sure you estimated the library sizes correctly? Try redundans, it is a pipeline that uses SSPACE, and it configures it automatically for you. ...
written 2.1 years ago by apelin20470
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Comment: C: Fisher's exact test gives p-value 0
... That number is still 0 when using any calculator. My question is, why is the p-value so low? The overlap is not that great, it is ~50-70% of genes. Is the 2x2 table constructed correctly? ...
written 2.1 years ago by apelin20470
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Check NGS data from NCI60 cell lines to confirm identity
... Hello, I have about 10x coverage of 3 different NCI60 cell lines, MCF7, 786-O and HT29. I am interested in using this NGS data to validate whether these cell lines are what they are, whether there is any contaminats (other cell lines). Is there any VCF file of these cell lines? Thanks. ...
illumina ngs nci60 written 2.1 years ago by apelin20470
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Comment: C: microRNA- sequencing analysis
... Smallest Illumina sequencing is 50bp as far as I know. Your microRNAs are going to be ~21-23nt. If you do not trim, half of your read will be adapter sequence and will prevent proper mapping. One question I do have however, is for step 4. I use bedtools multicov to see how many reads overlap with ma ...
written 2.2 years ago by apelin20470
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Comment: C: aligmnet of mutli-fasta fie to reference genome
... Run it on batches of 10 contigs... 1-10, 11-20, 21-30... see where the error is. Clearly it's one of the contigs, or maybe amount of contigs. ...
written 2.2 years ago by apelin20470
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Answer: A: Similarity between two sets of paired-end fastq files
... discoSNP... allows to compare SNPs between reads without a reference using Kmers ...
written 2.3 years ago by apelin20470
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Answer: A: Same BWA INDEX files for 0.7.12 and 0.7.13 versions?
... This was cross posted on Bio-bwa-help mailing list. The answer from Heng Li: > Yes, they are the same. > > Heng ...
written 2.3 years ago by apelin20470
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Comment: C: BBDuk trimming concern: large discarded, too aggressive (?)
... What was your input size? Try out instead of outm. ...
written 2.3 years ago by apelin20470
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Comment: C: Other RNA removal from RNA-Seq Data
... Why not first find out what is contaminating your data. Do a denovo transcript assembly, plot GC content of transcripts, see if you get multiple peaks. You can also blast your transcripts and find out if there are obvious contaminants. ...
written 2.3 years ago by apelin20470

Latest awards to apelin20

Centurion 2.5 years ago, created 100 posts.
Supporter 2.6 years ago, voted at least 25 times.
Popular Question 2.6 years ago, created a question with more than 1,000 views. For BLAST, setting maximum number of hits
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Alternative to MrBayes for BI phylogenetics?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Alternative to MrBayes for BI phylogenetics?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Alternative to MrBayes for BI phylogenetics?

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