Originally posted by chadn737
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Thanks a lot..!!
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Error occured in line 36 of file R13a_m_accepted_hits.sam. Error: ("'seq' and 'qualstr' do not have the same length.", 'line 36 of file R13a_m_accepted_hits.sam') [Exception type: ValueError, raised in _HTSeq.pyx:765]
>htseq-count .... >Released under the terms of the GNU General >Public License v3. Part of the 'HTSeq' framework, version 0.5.3p3.
>htseq-count .... >Released under the terms of the GNU General >Public License v3. Part of the 'HTSeq' framework, version 0.5.3p3.
awk '$11=="*"' accepted_hits.sam > noquals.sam; awk '$11 !~ /^\*$/' accepted_hits.sam > tmp.sam; awk 'FNR==NR{a[NR]=$10;next}{$11=a[FNR]}1' noquals.sam noquals.sam > tmp2.sam; awk -v OFS="\t" '$1=$1' tmp2.sam > tmp3.sam cat tmp.sam tmp3.sam > accepted_hits2.sam; rm tmp.sam tmp2.sam tmp3.sam noquals.sam;
$ htseq-count Traceback (most recent call last): File "/home/support/apps/cports/rhel-6.x86_64/gnu/HTSeq/0.5.3p6_Python_2.7.2/bin/htseq-count", line 3, in <module> import HTSeq.scripts.count File "/home/support/apps/cports/rhel-6.x86_64/gnu/HTSeq/0.5.3p6_Python_2.7.2/lib/python/HTSeq/__init__.py", line 8, in <module> from _HTSeq import * File "_HTSeq.pyx", line 11, in init HTSeq._HTSeq (src/_HTSeq.c:30228) ImportError: No module named pysam
$ htseq-count Traceback (most recent call last): File "/home/support/apps/cports/rhel-6.x86_64/gnu/HTSeq/0.5.3p6_Python_2.7.2/bin/htseq-count", line 3, in <module> import HTSeq.scripts.count File "/home/support/apps/cports/rhel-6.x86_64/gnu/HTSeq/0.5.3p6_Python_2.7.2/lib/python/HTSeq/__init__.py", line 8, in <module> from _HTSeq import * File "_HTSeq.pyx", line 11, in init HTSeq._HTSeq (src/_HTSeq.c:30228) ImportError: No module named pysam
sort 1: sort -T /scratch/vyellapantula -s -k 1,1 input.sam > sorted.sam sort 2: samtools sort input.bam sorted samtools view -h -o sorted.sam sorted.bam
< ENSG00000259158 14 --- > ENSG00000259158 23 51905c51905 < ENSG00000259165 15 --- > ENSG00000259165 30
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