User: BPors

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BPors40
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Posts by BPors

<prev • 23 results • page 2 of 3 • next >
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Comment: C: Searching for the common sequences in multiple (>2) fastq files
... Thank you for your reply! I would like to try this approach, however can you explain why should I look for minimum coverage regions? Because they(the common sites) would be more rare than the others? I couldnt understand, sorry ...
written 2.3 years ago by BPors40
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Searching for the common sequences in multiple (>2) fastq files
... Hi, I am trying to see that if my fastq files ( 15 of them) coming from different sources are sharing the same or very similar reads (allowing 1-2 mismatches), and then I would like to grab each whole sequence that they were sharing ( Even though they are sharing 50 bp, I want to grab the whole rea ...
fastq sequence align common written 2.3 years ago by BPors40 • updated 2.3 years ago by guillaume.rbt750
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Comment: C: Aligning short sequences to fastq
... Thank you! I have eventually used BBDUK but I will give bowtie a try soon with these options. ( -r). ...
written 2.3 years ago by BPors40
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Comment: C: Aligning short sequences to fastq
... Thank you! That worked well for me! ...
written 2.3 years ago by BPors40
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Comment: C: Aligning short sequences to fastq
... Thank you for your suggestion. Would this work if my reads are in text format? ...
written 2.3 years ago by BPors40
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Comment: C: Aligning short sequences to fastq
... Thank you for your answer. I would like to try, but I have these reads in just text format, therefore I cannot turn it to fastq. I think in Bowtie I have use reads in fastq format ...
written 2.3 years ago by BPors40
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Aligning short sequences to fastq
... Hi, I am trying to search for the presence of couple sequences (around 400) each with a size of 23 bps,in different fastq files, while allowing 1-2 mismatches at maximum. I am not sure if turning the fastq to a genome(transcriptome) would be a nice approach? I have tried making the fastq -> fast ...
short aligning sequences rna-seq written 2.3 years ago by BPors40
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Comment: C: Sorting samtools output by flag or grepping its tags
... Yes, followed the same thought, but then I cut the QNAME part, sorted and counted the unique ones in 256flagged bam file. Then I counted the unique QNAMEs in myfileSA_filtered.bam, and the numbers were still different ...
written 2.3 years ago by BPors40
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Comment: C: Sorting samtools output by flag or grepping its tags
... well, I wanted to retrieve the chimeric reads, so I thought to grab the ones which have another place to be. I have used bwa-mem -M -a to get all alignments, but since I have used -M, as a flag, I used 256 instead of 2048. Would it be a wrong choice? ...
written 2.3 years ago by BPors40
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Comment: C: Sorting samtools output by flag or grepping its tags
... Because I did not only use SA:Z, it also includes the accession number of the genome, therefore making it specific to its chimerics ...
written 2.3 years ago by BPors40

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Popular Question 21 months ago, created a question with more than 1,000 views. For How to remove certain samples from SummarizedExperiment dataset? (BioConductor)

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