User: hafiz.talhamalik
hafiz.talhamalik • 40
- Reputation:
- 40
- Status:
- New User
- Location:
- Pakistan
- Last seen:
- 3 days, 16 hours ago
- Joined:
- 3 years, 2 months ago
- Email:
- h***************@gmail.com
Posts by hafiz.talhamalik
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... What does Replicate array means? and how can I perform differential gene expression in R for this type of data ? What will be the experimental design for that ? ...
written 4 weeks ago by
hafiz.talhamalik • 40
• updated
14 days ago by
Biostar ♦♦ 20
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235
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... oho. M really sorry for that..! ...
written 7 weeks ago by
hafiz.talhamalik • 40
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235
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... oh okz.. Thanks for this. let me go through this.
so in a nutshell you are suggesting samtool's aprroach is not good for this kind of analysis ? ...
written 7 weeks ago by
hafiz.talhamalik • 40
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... yes assembled genomes. ...
written 7 weeks ago by
hafiz.talhamalik • 40
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... I have downloaded all the fasta sequence of salmonella from ncbi and now i want to compare snp's from those fasta files with my sequenced data's vcf file. ...
written 7 weeks ago by
hafiz.talhamalik • 40
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... samtools flagstat
4908 + 0 in total (QC-passed reads + QC-failed reads)
4 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
4761 + 0 mapped (97.00% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itse ...
written 7 weeks ago by
hafiz.talhamalik • 40
• updated
7 weeks ago by
finswimmer ♦ 8.9k
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... samtools --version
samtools 1.8
Using htslib 1.8
---
bcftools --version
bcftools 1.8
Using htslib 1.8
---
samtools view -H my-sorted.bam
@HD VN:1.3 SO:coordinate
@SQ SN:NC_003198.1 LN:4809037
@PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa mem -M ...
written 7 weeks ago by
hafiz.talhamalik • 40
• updated
7 weeks ago by
finswimmer ♦ 8.9k
0
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1
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235
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... yeah I tried that. sorted bam file is fine. ...
written 7 weeks ago by
hafiz.talhamalik • 40
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1
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235
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... completely blank one. no header, nothing ...
written 7 weeks ago by
hafiz.talhamalik • 40
0
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1
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235
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1
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... yes i tried them separately but still empty file. ...
written 7 weeks ago by
hafiz.talhamalik • 40
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