User: blooming.daisy333

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Posts by blooming.daisy333

<prev • 23 results • page 1 of 3 • next >
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extracting spesific sequences from bam or bam.bai file using samtools
... im using samtool to extract specific regions from the sorted bam file/bam.bai file. e.g if i want to extract the sequence from 329729 to 329840 of chromosome one, then how would i proceed??? the command that im using is ./samtools view alignment.sorted.bam gnl|BGIA2|CA_chr1:329729-329840 ...
next-gen written 20 hours ago by blooming.daisy3330
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splice junction information with hisat2
... I am newbie to linux and NGS. Can anyone help me out how to get information about splice junctios using HISAT2??? the command im using is giving information in single file about alignment in SAM format. the command is as follows: ./hisat2 -p 64 --max-intronlen 10000 -x /data/memona/hisat2-2.1 ...
next-gen written 23 hours ago by blooming.daisy3330
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Comment: C: alignment with HISAT2
... thank you so much Devon. you ve correctly pointed out the mistake. it worked ...
written 23 hours ago by blooming.daisy3330
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alignment with HISAT2
... i am using following command to align the reads in hisat2: for my project [memona@farooq hisat2-2.1.0]$ ./hisat2 –p 64 --max-intronlen 10000 –x /data/memona/hisat2-2.1.0/hisat_index -1 /data/memona/SRR959590_A_1P.fq -2 /data/memona/SRR959590_A_2P.fq –S /data/memona/hisatresult/hisat_align.sam ...
next-gen written 1 day ago by blooming.daisy3330 • updated 1 day ago by Devon Ryan78k
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Comment: C: building index with HISAT2
... thank you sooo much it for your kind guidance and precious time. It has worked out in index output files. but now i am facing problem in alignment with HISAT2. i am using following command [memona@farooq hisat2-2.1.0]$ ./hisat2 –p 64 --max-intronlen 10000 –x /data/memona/hisat2-2.1.0/hisat_inde ...
written 1 day ago by blooming.daisy3330
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Comment: C: building index with HISAT2
... i have spesified path to each file as follows : ./hisat2-build –p 64 /data/memona/reference/1.fa,/data/memona/reference/2.fa,/data/memona/reference/3.fa,/data/memona/reference/4.fa,/data/memona/reference/5.fa,/data/memona/reference/6.fa,/data/memona/reference/7.fa,/data/memona/reference/8.fa,/d ...
written 1 day ago by blooming.daisy3330
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Comment: C: building index with HISAT2
... thank you so much for the kind guidance. it really worked to give me the 8 index output files. but name of the output files are : 2.fa.1.ht2, 2.fa.2.ht2, v, 2.fa.3.ht2, 2.fa.4.ht2, 2.fa.5.ht2, 2.fa.6.ht2, 2.fa.7.ht2, 2.fa.8.ht2 rather to the name specified in command "hisat_index"... is that inde ...
written 1 day ago by blooming.daisy3330
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building index with HISAT2
... I am newbie to linux and NGS. Whle trying to build an index with hisat2 for my project, im getting following error: "Error: could not open 2.fa Total time for call to driver() for forward index: 00:00:00 Error: Encountered internal HISAT2 exception (#1) Command: hisat2-build --wrapp ...
next-gen written 1 day ago by blooming.daisy3330 • updated 1 day ago by Thibault D.500
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Comment: C: junction.bed output files from tophat
... thank you so much for the help... ...
written 6 days ago by blooming.daisy3330
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junction.bed output files from tophat
... im newbie to NGS and linux. I have used Tophat to determine the splice junction in my sequences. i want to know that how could i play with junctions.bed output file of tophat? Actually I want to develop a PWM (position weight matrix) from this data. for which i need to extract 13 nucleotides (3 fro ...
next-gen written 6 days ago by blooming.daisy3330 • updated 6 days ago by WouterDeCoster27k

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