User: Yijun Tian

gravatar for Yijun Tian
Yijun Tian20
Reputation:
20
Status:
New User
Location:
Medical College of Wisconsin
Last seen:
9 months, 3 weeks ago
Joined:
2 years, 6 months ago
Email:
a*********@163.com

Posts by Yijun Tian

<prev • 22 results • page 1 of 3 • next >
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Chimeric read insert length in SAM $9
... Hello everyone, I am recently doing a script to dissect chimeric alignment from BAM file, here is my code: #!/bin/bash samtools=`which samtools` bn=$(basename $1 .bam) echo processing $bn $samtools view -@ 20 -h -b -f97 -F22 $1 > $bn.flag97.bam $samtools view -@ 20 -h -b ...
alignment written 9 months ago by Yijun Tian20
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Comment: C: extracting the soft clipped seq only from a sam file
... Hi Devon, Can you also add a feature for which end does the softclip reads comes from (5 Prime or 3 Prime) ? This one is very important for my downstream analysis and I've no idea about C... Thank you! ...
written 10 months ago by Yijun Tian20
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Comment: C: Comparing Two Bam Files Obtained From The Same Files And The Exact Settings
... Jvarkit is the mightiest. Hi Pierre. Do you think it's possible for CmpBams to give leftmost coordinates difference for certain read as well as CIGAR in two different alignment? I am trying to map clipped reads to find some circle split reads. ...
written 10 months ago by Yijun Tian20
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Comment: C: Remap Clipped Sequence
... Hi Tomas, I knew the post is very old. But can I know your solution for Remap Clipped Sequence? I am trying to remap the Clipped sequence for detecting some eccDNA from our NGS data. My strategy is exactly like yours. If I can follow some of your code to make it work on my data. That will be great h ...
written 10 months ago by Yijun Tian20
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Comment: C: How to extract reads with a known variant form a bam file
... Hi Pierre, Based on your answer. I've tried my best to write below script. Do you think it's right to using it for extracting the alignment with SNPx? final String contig= "chr17"; final int mutpos = 38256322; final char mutbase='T'; return records.stream().anyMatch(R->R.getRead ...
written 14 months ago by Yijun Tian20
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Comment: C: How to extract reads with a known variant form a bam file
... Hi Pierre, I have tried SortSam my BAM file by queryname with : java -jar ~/picard/build/libs/picard.jar SortSam I=22RV1-DHT_CTCF.bam O=22RV1-DHT_CTCF.psort.bam SORT_ORDER=queryname And when add --pair to the script you provide in samjdk and run as : java -jar dist/samjdk.jar --pair -f ...
written 14 months ago by Yijun Tian20
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Comment: C: How to extract reads with a known variant form a bam file
... Hello Pierre, Your script is very useful in my research. And is there a way to dissect with multiple-base pattern in a specified region from BAM file? (Like extract alignment with chr19:100000-100003 as ATCG in reverse strand). Another question is I noticed that in the manual of samjdk there is a s ...
written 14 months ago by Yijun Tian20
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Comment: A: TCGA PRAD Biochemical Recurrence Data Problem
... @Andy Lee Hi Andy, I noticed same problems for the biochemical recurrence data. Do you have a answer now? Yijun ...
written 15 months ago by Yijun Tian20
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Comment: C: To make difference or Ratio, it's a problem
... Well, I am thinking ratio might be a better way since normalizing RPKM or even TPM of gene A to gene B (both gene expression are obvious and the variations across samples are equal) may be able to give a more accurate evaluation of my prediction. Difference method seemed to be too crude in my questi ...
written 18 months ago by Yijun Tian20
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How to interpret ChIP-seq peak at cell line level?
... Hello everyone, I have a list of enriched peaks called from rigorous prepared ChIP-seq reads obtained by certain treatment which can activate specific transcription factor. The headers are: 1. RegionID 2. chr 3. start 4. end 5. -log10 q-value (QuEST) 6. -log10 p-value (QuEST) 7. Rank 8. Ch ...
chip-seq written 21 months ago by Yijun Tian20

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