User: Amitm

gravatar for Amitm
Amitm2.1k
Reputation:
2,070
Status:
Trusted
Location:
UK
Website:
http://www.linkedin.co...
Last seen:
an hour ago
Joined:
8 years, 11 months ago
Email:
a******@gmail.com

Posts by Amitm

<prev • 266 results • page 1 of 27 • next >
0
votes
2
answers
235
views
2
answers
Comment: C: STAR and StringTie to identify novel isoforms (please check my work)
... Hi, This STAR+StringTie workflow is able to detect novel transcripts as far as I can tell from my own experience with multiple datatypes (splicing defects, CRISPR knockouts etc.). But to be fair, I knew which gene to look at. So, I do not have an idea of how much novel stuff you can detect on averag ...
written 11 days ago by Amitm2.1k
0
votes
2
answers
235
views
2
answers
Comment: C: STAR and StringTie to identify novel isoforms (please check my work)
... Ok, this is new information as I had the impression that you have always used "Mus_musculus.GRCm38.100.gtf" as GTF file. The command set-up that you pointed out which didn't work, has gencode GTF has input instead. The genome file is the same in both case (and I am assuming it is from Ensembl and ha ...
written 19 days ago by Amitm2.1k
0
votes
2
answers
235
views
2
answers
Comment: C: STAR and StringTie to identify novel isoforms (please check my work)
... Ok, I see. Something is not right. Irrespective of whether a gene gets any count assigned or not, all of the IDs are present in the count file created. So, it should have ~55k lines (or, the number genes in the GTF file provided when STAR index was created). Just wondering if it could be possible t ...
written 21 days ago by Amitm2.1k
0
votes
2
answers
235
views
2
answers
Comment: C: STAR and StringTie to identify novel isoforms (please check my work)
... Hi, I am at my wit's end here, not sure where the problem is arising. Don't worry about IGV, as STAR is recognising splice junctions (predominantly known ones), so I think splice-aware alignment is happening. When you load BAM file into IGV, the default mode is where each read is visible (as a horiz ...
written 22 days ago by Amitm2.1k
1
vote
0
answers
118
views
0
answers
Comment: C: Error in GATK HaplotypeCaller
... On second thoughts, the BED file that you are providing is also worth checking. As a rule, given a standard BAM file, the sequence names in the header lines of that should match with all other sequence data inputs (genome fasta, BED file etc.) ...
written 23 days ago by Amitm2.1k
0
votes
0
answers
118
views
0
answers
Comment: C: Error in GATK HaplotypeCaller
... Hi, The error message is saying that there is a chromosome (in this case chr1_gl383516_fix) that is present in your input BAM (either in the header lines, or in the alignment, or both), that is not present in the genome fasta : ucsc.hg19.fasta you have provided. Check the header lines of your BAM us ...
written 23 days ago by Amitm2.1k
0
votes
2
answers
235
views
2
answers
Comment: C: STAR and StringTie to identify novel isoforms (please check my work)
... Yes, "Aligned.sortedByCoord.out.bam" is the file to look at using IGV. Why should you not see blue bridges.. if the read quality was ok (as per fastQC) and STAR says ~90% unique alignment. That is quite puzzling, to be honest. If there was a chance of contamination in the reads (some other organism. ...
written 23 days ago by Amitm2.1k
0
votes
2
answers
235
views
2
answers
Comment: C: STAR and StringTie to identify novel isoforms (please check my work)
... Hi, You are right, you do not need to have provided anything additional to STAR for strand-sensitivity. But for StringTie, you need to specify either the `--rf` or `--fr` param to indicate which strand is being sequenced. If you are not sure which strand has been sequenced, then you can identify th ...
written 23 days ago by Amitm2.1k
3
votes
1
answer
122
views
1
answers
Answer: C: Detecting CNVs from BAM file
... Hi, At the least if you have a test and a control sample (BAM), then you can try [Galaxy][1]. Its a website with all sorts of tools for genomic data manipulation, but without needing to use programming/ command-line tools. You would need to upload your files there, of course. There is sufficient do ...
written 23 days ago by Amitm2.1k
1
vote
2
answers
235
views
2
answers
Answer: A: STAR and StringTie to identify novel isoforms (please check my work)
... Hi, Since you have 100bp PE reads (that too in good lib. size), you should use additional confidence measures for alignment in STAR. In the STAR [manual][1], look at the `ENCODE options` section. Specifically `--outFilterType` and `--alignSJoverhangMin` are worthwhile in keeping false +ve rate low i ...
written 24 days ago by Amitm2.1k

Latest awards to Amitm

Teacher 23 days ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 4 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: How to decide the quality of RNA-seq analysis
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Popular Question 9 months ago, created a question with more than 1,000 views. For Removing PCR primers in targeted sequencing with nested amplicons
Scholar 11 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 11 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Scholar 11 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
Scholar 2.5 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 2.9 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Scholar 3.0 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
Good Answer 3.4 years ago, created an answer that was upvoted at least 5 times. For A: Kmer Content in FastQC failed
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Removing PCR primers in targeted sequencing with nested amplicons
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 3.7 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Good Answer 3.9 years ago, created an answer that was upvoted at least 5 times. For A: Kmer Content in FastQC failed
Scholar 4.3 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1929 users visited in the last hour
_