User: MAPK

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MAPK1.0k
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Posts by MAPK

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Comment: C: Aligning multiple short reads with multiple long reference reads
... I did use bowtie, but the problem arises when it extracts lots of sequences that are not exact match ( it allows for too many mismatches as well). My sequenses are srna reads and I want to align them to retrotransposons (LTR) regions. I have about a thousand LTR sequences and they are a few hundred ...
written 9 days ago by MAPK1.0k
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Comment: C: Aligning multiple short reads with multiple long reference reads
... Hehe Just got confused. So basically can use BWA? ...
written 9 days ago by MAPK1.0k
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Aligning multiple short reads with multiple long reference reads
... Hi, I was wondering if there a way to align short reads with multiple long reads and see a long stretch of aligned region from the same genome? I have millions of short reads and I want to align those short reads to thousands of long sequences from the same genome and see the aligned region. Thanks ...
alignment written 9 days ago by MAPK1.0k
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Comment: C: Convert sequence file to fasta format using python
... Thanks to everyone, all answers accepted! Wasn't aware of this feature. I was thinking it was similar to stackoverflow where you have option to accept only one answer. ...
written 11 days ago by MAPK1.0k
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Comment: C: Convert sequence file to fasta format using python
... Thanks, but it does not increase the fasta identifier as `>1`, `>2`, `>3`.... All sequences are named `>1`. ...
written 11 days ago by MAPK1.0k
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Convert sequence file to fasta format using python
... Hi I am new in python and want to see how this can be done in python (I can do this in R). I have a text file `myfile.txt` with one column and thousands of rows as shown below. I want to convert this to fasta `result.fasta` format as shown below. How can I do this in python? `myfile.txt` ATGTG ...
python written 11 days ago by MAPK1.0k • updated 11 days ago by Matt Shirley7.8k
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Using DESeq2 for RNAseq analysis for two samples and a control with two replicates each
... Hi Everyone, I have 2 different samples and one Control (Sample_A, Sample_B and Control) and two replicates for each. So the data matrix I have contains six different columns for fold counts for Sample_A1, Sample_A2, Sample_B1, Sample_B2, Control_1, Control_2. I want to know how I can use [DESeq2][1 ...
rnaseq written 18 days ago by MAPK1.0k • updated 18 days ago by Asaf4.4k
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Comment: C: DESeq2 R package to perform RNAseq analysis
... Thanks for your answer. While it says about utilizing log2 fold change of B vs A, of C vs A, and of C vs B, it does not mention about how it treats replicates. Since I have three samples but with two replicates, I am not sure how this is going to be useful. ...
written 20 days ago by MAPK1.0k
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Comment: C: Barcode and Adapter sequences in sRNAseq data
... @genomax Thank you for your answer. Yes I want to remove the adapter sequences and keep the actual reads only. As in this fastq file here-https://ibb.co/iENdP5, is it not that I also have to trim the 6 bases (ACTTGA bases) on the second line in fastq file? ...
written 25 days ago by MAPK1.0k
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Barcode and Adapter sequences in sRNAseq data
... Hi Everyone, I am new to RNAseq data. I am working on sRNAseq data and I am trying to start with adapter trimming part. I want to understand whether I have to remove the barcode region (the first 6 bases) from the reads in my sRNAseq data. I have done the alignment of 3 different reads and adapter, ...
rna-seq written 25 days ago by MAPK1.0k

Latest awards to MAPK

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