User: linjc.xmu

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linjc.xmu10
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3 years, 11 months ago
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Posts by linjc.xmu

<prev • 23 results • page 2 of 3 • next >
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filter internal priming events in oligdT based Reverse transcription of 3'end library
... Hi. Is there any way to use samtools or bedtools to filter internal priming from BAM file? The principle is: within -10 nt and +10 nt window of the first base of unique mapped reads, if there has AAAAA (five continuous As or more than five As), this read should be filter out from BAM file. Thank you ...
rna-seq written 19 months ago by linjc.xmu10
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STAR set --sjdbOverhang value
... Dear all, STAR manual said set --sjdbOverhang at readlength-1. I am confused by this with two questions. 1. If I generated genome index by setting it at 100 previously, and now I have a PE150 reads, should I re-generate genome index by setting it at --sjdbOverhang 149? 2. If I use --clip3pNbases 5 ...
rna-seq written 22 months ago by linjc.xmu10 • updated 22 months ago by swbarnes27.9k
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STAR --quantMode GeneCounts function
... Dear all, Does STAR 2.6 `--quantMode GeneCounts` only quant unique mapping reads? How to specialize it only quant the unique mapped reads? Thanks a lot. ...
rna-seq written 22 months ago by linjc.xmu10 • updated 22 months ago by RamRS27k
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Comment: C: De-multiplex of no illumina index RNAseq libraries on Novaseq
... Thanks. Do you mean it's better to get data from Undetermined one? ...
written 22 months ago by linjc.xmu10
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Comment: C: De-multiplex of no illumina index RNAseq libraries on Novaseq
... Yes. The barcode location is right. My insertion size is ~180-375 bp. Read length is PE150. Sequencing facility sent me G8 data split by my barcode. But the unique mapping rate is low (~47%), multi-alignment rate is ~50%. Usually, I got 90% unique mapping for arabidopsis samples on Hiseq2500. So I a ...
written 22 months ago by linjc.xmu10
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Comment: C: De-multiplex of no illumina index RNAseq libraries on Novaseq
... Thanks. Sequencing company said Novaseq generates a GGGGGG index file (reads) naturally. What's this? ...
written 22 months ago by linjc.xmu10
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De-multiplex of no illumina index RNAseq libraries on Novaseq
... Dear all, I made a set of RNA-seq libraries without illumina index embedded, but with inner barcode right after read 1 sequences. Now they were sequenced on Novaseq platform with others libraries. Where could I get my data? In undetermined data, or in the data marked by GGGGGG index? Thanks a lot. ...
sequencing written 22 months ago by linjc.xmu10 • updated 22 months ago by Devon Ryan95k
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Comment: C: output unmapped file in STAR alignment
... STAR_2.5.3a, thanks. ...
written 22 months ago by linjc.xmu10
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output unmapped file in STAR alignment
... Hi All. I am using STAR alignment to remove rRNA reads, and collect unmapped reads for further alignment. My command line is: STAR --genomeDir ./genome/index/rRNA/ --readFilesIn RA1_R1.fastq RA1_R2.fastq --clip3pNbases 12 --clip5pNbases 50 --outFileNamePrefix rRNA1 --outReadsUnmapped Fastx However, ...
alignment written 22 months ago by linjc.xmu10
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Comment: C: PCA plot from read count matrix from RNA-Seq
... Thank you very much! ...
written 23 months ago by linjc.xmu10

Latest awards to linjc.xmu

Popular Question 12 months ago, created a question with more than 1,000 views. For STAR --quantMode GeneCounts function
Popular Question 18 months ago, created a question with more than 1,000 views. For RNA-seq library/Gel purification/bioanalyzer

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