User: kspata

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kspata10
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Posts by kspata

<prev • 15 results • page 1 of 2 • next >
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Methylation Status of CpG islands for a specific gene
... Hi, I am looking to obtain % Methylated C's for CpG islands for a specific gene. I have some BS converted PCR amplicon sequences sequenced on NextSeq PE150. I am using human genomic sequence for that particular gene X as a reference. I am using the following pipeline. > 1. Raw Reads > 2. bis ...
gene R methylkit bismark bs written 3 days ago by kspata10
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Comment: C: Calculate Mapping Rate for an alignment to each sequence of a multi-fasta refere
... Thank you for the suggestion. I will use these tools and align input data to a complete genome. ...
written 17 days ago by kspata10
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Comment: C: Calculate Mapping Rate for an alignment to each sequence of a multi-fasta refere
... I wish to know variants in my data with respect to this reference. But even though the alignment rate is low I was interested to know if mapping rates for each sequence in a multi-fasta reference file can be calculated using SAM or BAM file? ...
written 17 days ago by kspata10
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Comment: C: Calculate Mapping Rate for an alignment to each sequence of a multi-fasta refere
... These are the results for samtools idxstats input.sorted.bam X1 3580 9483 0 X2 2836 8110 0 X3 2188 8220 0 X4 1468 6698 0 * 0 0 0 These are the results of samtools flagstat samtool ...
written 17 days ago by kspata10
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Comment: C: Calculate Mapping Rate for an alignment to each sequence of a multi-fasta refere
... The reference is sequence of 4 transcripts. I performed a BLAST and came to know it mapped closely to immunoglobulin light and heavy chain. This is all the information which I could gather. ...
written 17 days ago by kspata10
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Comment: C: Calculate Mapping Rate for an alignment to each sequence of a multi-fasta refere
... Thank you for replying. These are the numbers from my data. The multi fasts file reference which I used is a synthetic construct. The total mRNA data was mapped to this reference. The data is Miseq with PE 300. What can I do to increase the mapping rate.? I used bowtie2 with -I 0 and -X 1000 with -f ...
written 18 days ago by kspata10
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Calculate Mapping Rate for an alignment to each sequence of a multi-fasta reference
... Hi, I have aligned a sample PE RNA-seq data to a multi-fasta reference. I wish to find out mapping rate for each sequence of the multi-fasta reference. How can I extract that information from SAM or BAM file? I have bowtie2 mapping rate for the overall alignment. **6259700** reads; of these: ...
flagstat samtools rna-seq mapping rate bowtie2 written 18 days ago by kspata10 • updated 17 days ago by h.mon15k
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Comment: C: Convert blastn to gff3
... Hi I am open to use a parser as well.. the question is just how to write it? ...
written 13 months ago by kspata10
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Convert blastn to gff3
... Hi I have the output of blastn in a tabular format. I need to convert this into a gff3 format. How to write a parser for this or how can i do it without parser? ...
gff3 blastp blastn written 13 months ago by kspata10
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Comment: C: CRISPR repeat identification tool comparison
... I compared both tools on multiple reference samples and compared the output for exact matches with crispr database. I then discarded the tool which gave over-prediction of the putative crispr arrays. I found piler-CR to be better at crispr prediction than crt for my sample. ...
written 14 months ago by kspata10

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