User: imlituan

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imlituan20
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Posts by imlituan

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how to get exact break point in COSMIC fusion gene?
... there's one item in COSMIC fusion Mutation Id COSF463 Type This fusion structure is derived from the range of fusion mRNAs reported. Translocation Name EML4{ENST00000318522}:r.1_1751_ALK{ENST00000389048}:r.4080_6220 How to infer the exact breakpoint from the this item, like 'chr:xxxxxxxx' ...
genome next-gen rna-seq sequencing written 9 weeks ago by imlituan20 • updated 9 weeks ago by chen1.1k
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Tutorial: How to select reads with specific flag using samtools
... In sam and bam files, flag is used to indicate the alignment state of the read, each flag has 11 positions when expressed as binary numbers, and each position indicates a specific attribute, which is shown below, 0x1 represents the first position, 0x400 represents the 11th position. At each positio ...
tutorial next-gen sequencing written 10 weeks ago by imlituan20
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Comment: C: What does the reference_id = -1 indicate in a .sam file read with pysam?
... I did a test using a random read, which won't map to the reference. I then check this unmapped read, its reference_id is -1. ...
written 12 weeks ago by imlituan20
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how to select the best combination of gap_open and gap_extention in pairwise sequence alignment?
... I recently use clustal omega to make a multiple alignment and get the pairwise identity matrix. Then I use the needle to align two sequences from this msa. I find that, the identity from needle alignment is lower than that from msa. I think it may be the result of bad parameters of needle. Then i wr ...
alignment written 12 months ago by imlituan20

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