User: BPors

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BPors30
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Posts by BPors

<prev • 18 results • page 1 of 2 • next >
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How to compare the expression of a gene for some samples compared to the rest of the samples?
... I am trying to see the distribution of expressions of certain genes for certain patients, and want to compare them for the rest of the patients. For example, for 4 genes and 50 patients, some have values and some has no information for gene expression (empty): IDs Patient1 Patient2 ... ...
gene expression rna-seq written 15 months ago by BPors30
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Retrieving coverage image
... Hi! I am trying to visualize the coverage of my gene expression using IGV, and, I want to retrieve a high resolution and compact IGV image. Or, with the usage of any other tools. I found that I can use DEGseq however I am not very fluent with R, therefore have not try it yet. Do you have any sugge ...
next-gen igv coverage rna-seq expression written 21 months ago by BPors30
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Answer: A: Extract Sequence From Fasta File Using Ids From A Separate File
... If you had only the sequences in the example.txt instead of the identifiers, how would you grab the identifiers and their sequences? ( in this case, the purpose was retrieving the sequences with identifiers, what I am asking is retrieving headers and sequencers with known sequences ...
written 21 months ago by BPors30
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Comment: C: Searching for the common sequences in multiple (>2) fastq files
... True..Many thanks for the explanation. Would you suggest the usage of samtools ? ...
written 21 months ago by BPors30
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Comment: C: Searching for the common sequences in multiple (>2) fastq files
... Sure thing. What I meant is, my reads are 150 bp each in all fastq files, and I want to get the reads which are shared by other fastq files. The ultimate goal would be to grab the ones which are matching in more than 140 bps. However, I can put this threshold to 50 bp. So, if the read1 from fileA.fa ...
written 21 months ago by BPors30
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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 21 months ago by BPors30
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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 21 months ago by BPors30 • updated 21 months ago by guillaume.rbt590
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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 21 months ago by BPors30
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Comment: C: Aligning short sequences to fastq
... Thank you! That worked well for me! ...
written 21 months ago by BPors30
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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 21 months ago by BPors30

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