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Search: Posts Made By: scami
Forum: Bioinformatics 12-31-2017, 03:55 AM
Replies: 0
Views: 635
Posted By scami
interproscan last forever

Dear community,
i am using interproscan to find the domains within my proteins. i ran the software without any error message. However, the job seems to last forever although my input file only...
Forum: Bioinformatics 10-10-2017, 12:17 AM
Replies: 0
Views: 479
Posted By scami
Total counts in eXpress

Dear aa,
I am using express to calculate the fpkm after aligning my RNAseq paired ends reads on a transcriptome with bwa. After mapping I got around 42 millions reads mapped (mapped in proper pair)....
Forum: Bioinformatics 02-04-2016, 08:11 AM
Replies: 0
Views: 674
Posted By scami
HMMER search with Conserved Domain Database

Dear All,



I am trying to identify conserved domains in my proteins. I would like to use the Conserved domain database (CDD) since I know it is the most complete, and I would like to the my...
Forum: Bioinformatics 10-23-2015, 02:12 AM
Replies: 0
Views: 709
Posted By scami
Search specific blast database regions

Hi there,

I am using blastn in command line. I have a genome and created a blast database out of it with makeblastdb
During the pipeline I am developing I need to blast some sequence versus...
Forum: Bioinformatics 10-01-2015, 05:25 AM
Replies: 6
Views: 2,263
Posted By scami
Yes I did. I also thought I messed up the...

Yes I did. I also thought I messed up the reference genome file while removing the unwanted chromosomes with my python software. However afterwards I calculated the GC content of the chromosomes in...
Forum: Bioinformatics 09-30-2015, 10:42 PM
Replies: 6
Views: 2,263
Posted By scami
Thanks for the advice. I ran the command you...

Thanks for the advice. I ran the command you suggested and this is my result:
I divided the number of line of my fastq files in order to get the number of reads. I got a total of 187,595,025 reads....
Forum: Bioinformatics 09-30-2015, 09:14 AM
Replies: 6
Views: 2,263
Posted By scami
Hi GenoMax thanks for your reply. Parameters...

Hi GenoMax

thanks for your reply. Parameters are exactly the same for the two alignments. I used bwa with the default setting except I used 0.05 as edit distance. I then used samtools to convert...
Forum: Bioinformatics 09-30-2015, 08:59 AM
Replies: 6
Views: 2,263
Posted By scami
Sam file smaller than fastq

Hi Guys,

I hope it does not turn as a stupid question but this issue is driving me crazy. I have a reference genome A that contains chromosome I am not interested in. I used a python software to...
Forum: Bioinformatics 10-30-2014, 11:34 AM
Replies: 6
Views: 1,207
Posted By scami
Thanks

Thanks for the answer. Sam files I am using are very large so an ad hoc C or python script would not be the best option for me. I'll work on it anyway, thanks for the advice
Forum: Bioinformatics 10-30-2014, 08:32 AM
Replies: 9
Views: 1,806
Posted By scami
I agree with Brian actually. I would not trust...

I agree with Brian actually. I would not trust snps and indels called with such a low coverage in the absence of a reference genome
Forum: Bioinformatics 10-30-2014, 08:16 AM
Replies: 4
Views: 1,473
Posted By scami
Hi there, If you are familiar with...

Hi there,

If you are familiar with programming you could write a simple script. ALternatively you can open the fasta file with a text editor under linux and try this:
1) Find and replace \nA with...
Forum: Bioinformatics 10-30-2014, 08:10 AM
Replies: 9
Views: 1,806
Posted By scami
Hi bioman1, if I were you I would proceed...

Hi bioman1,

if I were you I would proceed with annotation first, that is finding the coding sequences in your assembled genome. Number of found genes will give you an idea of how good is your...
Forum: Bioinformatics 10-30-2014, 07:52 AM
Replies: 6
Views: 1,207
Posted By scami
Help with sam flags

Hi guys
I would like to ask you a help with the sam format flag. I am using samtools to extract reads from a bam file. Briefly I need to extract all mapped reads in a certain range which is easy to...
Forum: Bioinformatics 08-29-2014, 12:16 AM
Replies: 2
Views: 1,618
Posted By scami
Thanks

Thanks a lot! Yes sorry I used sampe and samse all the way around. You answer clarifies everything.
Cheers
Forum: Bioinformatics 08-28-2014, 10:44 PM
Replies: 4
Views: 1,753
Posted By scami
May be indexing.....

Hi Guys
the N in the consensus may me due to a missing indexed reference file. Try the following:



samtools index alignmentFile.bam



and then try the mpileup command again.
Forum: Bioinformatics 08-28-2014, 10:32 PM
Replies: 3
Views: 1,179
Posted By scami
Thanks!

Thanks for sharing this link! It sounds interesting! I will try it on my pipeline!
Forum: Bioinformatics 08-28-2014, 10:27 PM
Replies: 0
Views: 908
Posted By scami
bwa multiple alignment

Hi Guys,
a question about multiple alignment with bwa and coverage. Let's say I use the flag -n 2 when running bwa samse and for a couple of (not necessarely mated ) reads I get the following...
Forum: Bioinformatics 08-28-2014, 10:13 PM
Replies: 2
Views: 1,618
Posted By scami
Bwa, sampe vs samse

Hi guys,

this is probably a silly question. If I run bwa sampe I will get an alignment file which report informations about the paired end reads being in the expected pairing mode on the reference...
Forum: Bioinformatics 08-28-2014, 10:05 PM
Replies: 2
Views: 1,322
Posted By scami
Hi Ben, whats your question exactly? Do you...

Hi Ben,

whats your question exactly? Do you want to understand the difference between sampe and samse?
Forum: Bioinformatics 05-25-2014, 02:33 AM
Replies: 4
Views: 1,510
Posted By scami
Thanks!

I am not a great expert of this statistical test but I will have a look at it. Any further suggestions will be appreciated.
Forum: Bioinformatics 05-23-2014, 06:49 AM
Replies: 4
Views: 1,510
Posted By scami
Association study

Dear all,

I have a locus of around 4000bp and I know that this locus is involved in showing a certain phenotype, lets call it phenotypeA.
I have resequenced 8 organisms of the same species, 4...
Forum: Bioinformatics 05-04-2014, 11:26 PM
Replies: 3
Views: 1,676
Posted By scami
Thanks for the answer. Your suggestion led me to...

Thanks for the answer. Your suggestion led me to the right way. As a matter of fact I used fastq-dump to extract the sra sequence file. Although they were paired end I did not use the --split-files...
Forum: Bioinformatics 05-04-2014, 12:04 AM
Replies: 0
Views: 724
Posted By scami
Reference genome simulated data

Hi guys
I would like to test a tool for finding large copy number variations. I have a reference genome and I would like to simulate a new genome with long portions (from 1Kb to several Kb) that...
Forum: Bioinformatics 05-04-2014, 12:01 AM
Replies: 3
Views: 1,676
Posted By scami
Indexing with bwa and samtools

Hi guys!

I indexed a reference genome with the bwa index command. I then aligned a fastq file on it and obtained several gigabytes sam alignment file. When I use the "samtools mpileup" command I...
Forum: Bioinformatics 04-01-2014, 12:58 AM
Replies: 2
Views: 857
Posted By scami
Thanks sphil! I appreciated it!

Thanks sphil! I appreciated it!
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