User: genya35

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genya3510
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Posts by genya35

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Comment: C: aligning with igblast
... i have no problem with running igblast, however, it's not returning this particular del as a match for J region. Thanks ...
written 22 days ago by genya3510
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aligning with igblast
... Hello, I'm having a difficult time aligning the following sequence of IGK gene to a reference using igblast. It works with other tools but I must use igblast since it's part of the pipeline. Could someone please suggest how to tweak the parameters to get it to align? Thanks >test_sequ ...
alignment written 22 days ago by genya3510
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blastn output format with full subject's sequence
... Hello, Is there an outfmt option for blastn that will return the full subject's sequence in tubular format? I have tried outfmt 6 but it i don't see an option of returning the full subject's sequence. Thanks ...
sequence written 3 months ago by genya3510 • updated 3 months ago by h.mon26k
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Comment: C: how to identify degenerate primers in reads
... @genomax There is too much variation in the first 3 bases of each read. Is there a way to tell reformat.sh to ignore the first three bases and look at the base 4 to 23? thanks ...
written 3 months ago by genya3510
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Comment: C: how to identify degenerate primers in reads
... This was really helpful, however, I ended up with 1560 unique sequences. Is there a tool that would group them based on the similarity? ...
written 3 months ago by genya3510
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Comment: C: how to identify degenerate primers in reads
... I have a bunch of sequences that I'm trying to figure out at which base they are ambiguous. I wonder if there is a tool that can help with that. AAGGATCCGGCAGCCCCC ACGGATCCGGCAGCCCCC AGGGATCCGGCAGCCCCC ATGGATCCGGCAGCCCCC CAGGATCCGGCAGCCCCC CGGGATCCGGCAGCCCCC GAGGATCCGGCA ...
written 3 months ago by genya3510
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Comment: C: how to identify degenerate primers in reads
... it's an amplicon based assay. By primer sequence I mean "NNCTGGGTCCGCCAAGCT". Thanks ...
written 3 months ago by genya3510
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how to identify degenerate primers in reads
... Hello, I have a two adapter trimmed Illumina fastq files (read1 and read2). I would like to identify the primer sequence. I have some idea what the primer sequences are however, they appears to be degenerate. So far I've found over 200 variations for the primer sequence in reads and looking for a ...
next-gen written 3 months ago by genya3510 • updated 15 hours ago by Biostar ♦♦ 20
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Comment: C: group reads by sequence length
... the same platforms but different primers for each framework, (Miseq Illumina, average length of read is 168 after joining the two reads.) I will not know the exact range of size for each framework but the sequence size from the three frameworks will not overlap. I was hoping to find a tool that woul ...
written 3 months ago by genya3510
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group reads by sequence length
... Hello, I have two Illumina fastq files (read 1 and read 2) that contain reads from three different frameworks. Each framework has a different sequence length distribution from the other two. Are there any existing tools that can separate each framework into a separate file based on the sequence l ...
next-gen written 3 months ago by genya3510

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